# Patent

## Title
Methods and kits for isolation and analysis of a chromatin region

## Abstract

The present invention encompasses methods of identifying proteins and protein modifications of proteins specifically associated with a chromatin.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a US non-provisional that claims priority to U.S. provisional application 61/726,936 filed Nov. 15, 2012 and U.S. provisional application 61/875,969 filed Sep. 10, 2013, each of which is hereby incorporated by reference in its entirety.


GOVERNMENTAL RIGHTS
This invention was made with government support under R01DA025755, F32GM093614, P20RR015569, P20RR016460, U54RR020839, and UL1 TR000039 awarded by the National Institutes of Health. The government has certain rights in the invention.


FIELD OF THE INVENTION
The invention describes methods of identifying proteins and post-translational modification of proteins specifically associated with a chromatin region.
REFERENCE TO SEQUENCE LISTING
A paper copy of the sequence listing and a computer readable form of the same sequence listing are appended below and herein incorporated by reference. The information recorded in computer readable form is identical to the written sequence listing, according to 37 C.F.R. 1.821(f).
BACKGROUND OF THE INVENTION
It has long been appreciated that chromatin-associated proteins and epigenetic factors play central roles in gene regulation. Mis-regulation of chromatin structure and post-translational modification of histones (PTMs) is linked to cancer and other epigenetic diseases. The field of epigenomics has been transformed by chromatin immunoprecipitation approaches that provide for the localization of a defined protein or post-translationally modified protein to specific chromosomal sites. However, the hierarchy of chromatin-templated events orchestrating the formation and inheritance of different epigenetic states remains poorly understood at a molecular level; there are no current methodologies that allow for determination of all proteins present at a defined, small region of chromatin. Chromatin immunoprecipitation (ChIP) assay shave allowed better understand genome-wide distribution of proteins and histone modifications within a genome at the nucleosome level. However, ChIP assays are largely confined to examining singular histone PTMs or proteins rather than simultaneous profiling of multiple targets, the inability to determine the co-occupancy of particular histone PTMs, and that ChIP is reliant on the previous identification of the molecular target. Other chromatin immunoprecipitation methodologies do not provide a mechanism for determining the specificity of protein interactions, or do not enrich for a small integrated genomic locus and cannot detect protein contamination in purified material. Therefore, there is a need for methods that allow for determination of all proteins and protein posttranslational modifications specifically associated at a defined, small region of chromatin.
Reference To Color Figures
The application file contains at least one photograph executed in color. Copies of this patent application publication with color photographs will be provided by the Office upon request and payment of the necessary fee.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 graphically depicts the chromatin affinity purification with mass spectrometry method. (A) The chromatin affinity purification with mass spectrometry (ChAP-MS) approach provides for the specific enrichment of a given chromosome section and identification of specifically associated proteins and post-translational modifications. A LexA DNA affinity handle was engineered just upstream of the GAL1 start codon in S. cerevisiae. Strains containing the LexA DNA binding site and a plasmid expressing LexA-PrA protein affinity handle were cultured in glucose or galactose to provide transcriptional repression or activation, respectively, and subjected to in vivo chemical crosslinking to trap protein interactions. Following shearing of the chromatin to  ̃1,000 bp, LexA-PrA was affinity purified on IgG-coated Dynabeads and coenriched proteins/post-translational modifications were identified by high-resolution mass spectrometry. (B) To control for nonspecifically enriched proteins, a strain lacking the LexA DNA binding site, but containing the LexA-PrA plasmid, was cultured isotopically heavy (13C615N2-lysine) in glucose or galactose and mixed equally with the corresponding isotopically light culture containing the LexA DNA binding site prior to cell lysis. Following affinity purification (AP) and mass spectrometric analysis, nonspecifically enriched proteins were identified as a 1:1 ratio of light to heavy lysine-containing peptides, while proteins specifically enriched with the chromosome section were identified with a higher level of isotopically light lysine-containing peptides.
FIG. 2 depicts a plot, a Western blot image and a plot showing DNA affinity handle for purification of a specific chromosome section. (A) S. cerevisiae strain LEXA::GAL1 pLexA-PrA was created by insertion of a LEXA DNA binding site upstream of the GAL1 start codon via homologous recombination. The pLexA-PrA plasmid was introduced into this strain and the constitutive expression of the LexA-PrA fusion protein was confirmed by western blotting for PrA. (B) Introduction of the LEXA DNA binding site does not impede GAL1 transcription. cDNA from wild-type or LEXA::GAL1 pLexA-PrA strains grown in glucose or galactose was used as a template for real time PCR analysis of GAL1 versus ACT1 gene transcription. Error bars are the SE of triplicate analyses.
FIG. 3 depicts plots and a diagram showing efficiency of GAL1 chromatin purification. (A) The effect of buffer stringency on purification of LexA-PrA with associated chromatin was evaluated with ChIP. Strain LEXA::GAL1 pLexA-PrA was subjected to ChIP using the following buffer with the reagents indicated on the graph: 20 mM HEPES (pH 7.4), 0.1% Tween 20, and 2 mM MgCl2. Enrichment of GAL1 DNA relative to ACT1 DNA was monitored by real-time PCR. (B) ChIP was used to measure the specificity of enrichment of LexA-PrA bound chromatin. Enrichment was monitored by real-time PCR with primer sets at the indicated chromosomal locations. (C) GAL1 chromatin is enriched in both glucose and galactose growth conditions. The relative efficiency of GAL1 enrichment was monitored by real-time PCR with primers targeted to the “0” position in panel (B) and to ACT1. The SE is indicated.
FIG. 4 depicts an image of an SDS-PAGE gel and mass spectra showing ChAP-MS analysis of GAL1 chromatin. (A) Enrichment of GAL1 chromatin under transcriptionally repressive glucose and active galactose growth conditions. Strain LEXA::GAL1 pLexA-PrA was grown in either glucose or galactose and subjected to affinity purification of GAL1 chromatin via LexA-PrA as detailed in FIG. 1. Addition of an equivalent amount of isotopically heavy (13C615N2-lysine) cells lacking the LexA DNA binding site provided for the identification of proteins specifically enriched with GAL1 chromatin. Proteins coenriching with LexA-PrA were resolved by SDS-PAGE and visualized by Coomassie-staining. Each gel lane was sliced into 2 mm sections. Gel slices were treated with trypsin and resulting peptides were analyzed by high-resolution mass spectrometry. (B-D) Representative high-resolution mass spectra from proteins and histone post-translational modifications identified from the purification of transcriptionally active GAL1 chromatin.
FIG. 5 depicts a plot showing proteins and histone post-translational modifications enriched with GAL1 chromatin. Proteins and histone post-translational modifications identified from the ChAP-MS analysis of GAL1 chromatin in the transcriptionally active galactose and repressive glucose growth conditions are listed in accordance to their percent isotopically light. Proteins or post-translational modifications were considered specifically enriched with GAL1 chromatin if the percent isotopically light was 2 SDs from the nonspecific baseline established by the average of contaminant ribosomal proteins. Other proteins shown to be specifically enriched, but not correlated to gene transcription, are averaged together and listed individually in Tables 4 and 5. The number of proteins averaged is shown in parentheses. The SD is indicated.
FIG. 6 depicts a plot showing the validation of proteins and histone post-translational modifications on GAL1 chromatin. ChIP was targeted to Gal3-TAP, Spt16-TAP, Rpb2-TAP, H3K14ac, and H3K36me3 under transcriptionally active galactose and repressive glucose growth conditions. ChIP to general H3 was used as a nucleosome occupancy control for each histone post-translational modification ChIP. Enrichment of the 5′ end of GAL1 DNA relative to ACT1 DNA was monitored by real-time PCR. The SE is indicated.
FIG. 7 depicts diagrams and graphs showing that TAL proteins can specifically enrich native chromatin sections. (A) Schematic overview of TAL-ChAP-MS technology. (B) A unique DNA sequence in the promoter region of GAL1 was used to design a specific binding TAL protein that contained a PrA affinity tag. (C) A pTAL-PrA plasmid was introduced into S. cerevisiae cells, and the constitutive expression of the TAL-PrA fusion protein was confirmed by western blotting for PrA. (D) Expression of TAL-PrA does not impede galactose-induced GAL1 transcription. cDNA from wild-type yeast and wild-type with a plasmid expressing PrA-tagged TAL (+pTAL-PrA) grown in glucose (Glu) or galactose (Gal) was used as a template for real time PCR analysis of GAL1 versus ACT1 gene transcription. Error bars are the standard deviation. (E-G) TAL-PrA specifically binds and enriches chromatin at the promoter of transcriptionally active GAL1. ChIP was performed to the PrA-tag in wild-type cells containing the TAL-PrA (+pTAL-PrA, light gray bars) and in wild-type control (dark gray bars). The efficiency of GAL1 enrichment relative to ACT1 was monitored by real-time PCR with primers targeted to the TAL binding site (‘0’) and to DNA sequences 2000 by up- and downstream (E). The standard deviation is indicated. (F) Under transcriptionally active conditions (galactose), TAL-PrA specifically enriched chromatin from the GAL1 promoter region relative to sequences 2 kb up- and downstream. (G) The TAL-PrA protein did not show enrichment of the GAL1 promter chromatin under transcriptionally repressive glucose growth conditions.
FIG. 8 depicts an image of an SDS-PAGE gel and graphs showing TAL-ChAP-MS analysis of GAL1 promoter chromatin from cells grown its galactose. (A) Proteins co-purifying with TAL-PrA targeted to the promoter region of GAL1 (+pTAL-PrA lane) and proteins non-specifically associating with the IgG-coated Dynabeads (wild-type lane) were resolved by SDS-PAGE/Coomassie-staining and identified by high-resolution mass spectrometry. (B) Proteins found by label-free proteomic analysis to be enriched by >2-fold with transcriptionally active GAL1 promoter chromatin are plotted in accordance to their ranked level of enrichment divided by the total number of enriched proteins (N). Highlighted are the top 10% of proteins (>15-fold enrichment) and histone PTMs enriched with GAL1 promoter chromatin. (C) ChIP was targeted to Spt16-TAP, Rpb2-TAP, Gal3-TAP and H3K14ac under transcriptionally active galactose (light gray bars) and repressive glucose (dark gray bars) growth conditions, ChIP to general H3 was used as a nucleosome occupancy control for H3K14ac ChIP. Enrichment adjacent to the TAL binding site in the promoter of GAL1 relative to ACT1 was monitored by real-time qPCR. The standard error is indicated.



DETAILED DESCRIPTION OF THE INVENTION
A method of isolating and identifying proteins associated with a target region of chromatin in a cell has been discovered. The method may also be used to identify post-translational modifications (PTMs) of proteins associated with a target chromatin in a cell. Advantageously, the method may be used to determine whether the association of the identified proteins with a chromatin in a cell is specific or non-specific. As used herein, “specifically associated” or “specific association” of a protein with a target chromatin refers to any protein in a cell that normally associates with a chromatin in a cell. In addition, and as illustrated in the examples, the method may be used to determine the role of proteins and post-translational modifications (PTMs) of proteins in chromatin function, including regulatory mechanisms of transcription, and the role of epigenomic factors in controlling chromatin function.
I. Method of ChAP-MS
In some aspects, the invention provides methods of isolating and identifying proteins specifically associated with a target chromatin. As described in Example 1 and FIG. 1, a method of the invention comprises isolating a target chromatin from a cell. As used herein, a “target chromatin” refers to a specific chromatin or a chromatin fragment that may be used in an application of the invention. According to the method, isolating the target chromatin isolates nucleic acid sequences and proteins, including proteins comprising posttranslational modifications, associated with the target chromatin. The proteins and posttranslational modifications of proteins associated with the target chromatin may then be identified, and a determination of which of the identified proteins and posttranslational modifications of proteins associated with a target chromatin isolated from a cell are specifically or non-specifically associated with the target chromatin is made.
To determine which of the identified proteins and posttranslational modifications of proteins associated with a target chromatin isolated from a cell are specifically or non-specifically associated with the target chromatin, a method of the invention provides two cell samples, or lysates derived from two cell samples, comprising the target chromatin, wherein proteins in one cell sample, but not both of the cell samples are metabolically labeled. Typically, the two cell samples are grown identically. In addition, the target chromatin in one of the cell samples or an extract from one of the cell samples is tagged. The two cell samples, or lysates derived from the cell samples of the invention are combined. The tagged target chromatin is isolated in the presence of the other cell sample or an extract from the other cell sample. Therefore, if a target chromatin of the invention is tagged in the unlabeled cell sample, proteins specifically associated with the tagged chromatin are unlabeled, and will be isolated in the presence of labeled proteins from the labeled cell sample. Alternatively, if a target chromatin of the invention is tagged in the labeled cell sample, the proteins associated with the tagged chromatin are labeled, and will be isolated in the presence of unlabeled proteins from the unlabeled cell sample.
As such, determining if a certain identified protein associated with the target chromatin is labeled, unlabeled, or a combination of labeled and unlabeled may determine if the protein was specifically associated with a target chromatin of the invention. If an identified protein comprises a mixture of labeled and unlabeled proteins, then that protein became associated with a target chromatin during the chromatin isolation procedure, and association of that protein with the target chromatin is not specific. If a target chromatin of the invention is isolated from the unlabeled cell sample, only unlabeled identified proteins associated with the target chromatin are specifically associated with the target chromatin. Alternatively, if a target chromatin of the invention is isolated from the labeled cell sample, only labeled identified proteins associated with the target chromatin are specifically associated with the target chromatin.
In some embodiments, a tagged target chromatin of the invention is isolated from an unlabeled cell sample, and unlabeled proteins associated with the target chromatin are specifically associated with the target chromatin. In other embodiments, a tagged target chromatin of the invention is isolated from a labeled cell sample, and labeled proteins associated with the target chromatin are specifically associated with the target chromatin.
(a) Cells
A target nucleic acid sequence may be isolated from any cell comprising the target nucleic acid sequence of the invention. A cell may be an archaebacterium, a eubacterium, or a eukaryotic cell. For instance, a cell of the invention may be a methanogen, a halophile or a thermoacidophile archaeabacterium, a gram positive, a gram negative, a cyanobacterium, a spirochaete, or a firmicute bacterium, a fungal cell, a moss cell, a plant cell, an animal cell, or a protist cell.
In some embodiments, a cell of the invention is a cell from an animal. A cell from an animal cell may be a cell from an embryo, a juvenile, or an adult. Suitable animals include vertebrates such as mammals, birds, reptiles, amphibians, and fish. Examples of suitable mammals include without limit rodents, companion animals, livestock, and primates. Non-limiting examples of rodents include mice, rats, hamsters, gerbils, and guinea pigs. Suitable companion animals include but are not limited to cats, dogs, rabbits, hedgehogs, and ferrets. Non-limiting examples of livestock include horses, goats, sheep, swine, cattle, llamas, and alpacas. Suitable primates include but are not limited to humans, capuchin monkeys, chimpanzees, lemurs, macaques, marmosets, tamarins, spider monkeys, squirrel monkeys, and vervet monkeys. Non-limiting examples of birds include chickens, turkeys, ducks, and geese. In some embodiments, a cell is a cell from a human.
In some embodiments, a cell may be from a model organism commonly used in laboratory research. For instance, a cell of the invention may be an E. coli, a Bacillus subtilis, a Caulobacter crescentus, a Mycoplasma genitalium, an Aliivibrio fischeri, a Synechocystis, or a Pseudomonas fluorescens bacterial cell; a Chlamydomonas reinhardtii, a Dictyostelium discoideum, a Tetrahymena thermophila, an Emiliania huxleyi, or a Thalassiosira pseudonana protist cell; an Ashbya gossypii, an Aspergillus nidulans, a Coprinus cinereus, a Cunninghamella elegans, a Neurospora crassa, a Saccharomyces cerevisiae, a Schizophyllum commune, a Schizosaccharomyces pombe, or an Ustilago maydis fungal cell; an Arabidopsis thaliana, a Selaginella moellendorffii, a Brachypodium distachyon, a Lotus japonicus, a Lemna gibba, a Zea mays, a Medicago truncatula, a Mimulus, a tobacco, a rice, a Populus, or a Nicotiana benthamiana plant cell; a Physcomitrella patens moss; an Amphimedon queenslandica sponge, an Arbacia punctulata sea urchin, an Aplysia sea slug, a Branchiostoma floridae deuterostome, a Caenorhabditis elegans nematode, a Ciona intestinalis sea squirt, a Daphnia spp. crustacean, a Drosophila fruit fly, a Euprymna scolopes squid, a Hydra Cnidarian, a Loligo pealei squid, a Macrostomum lignano flatworm, a Mnemiopsis leidyicomb jelly, a Nematostella vectensis sea anemone, an Oikopleura dioica free-swimming tunicate, an Oscarella carmela sponge, a Parhyale hawaiensis crustacean, a Platynereis dumerilii marine polychaetous annelid, a Pristionchus pacificus roundworm, a Schmidtea mediterranea freshwater planarian, a Stomatogastric ganglion of various arthropod species, a Strongylocentrotus purpuratus sea urchin, a Symsagittifera roscoffensis flatworm, a Tribolium castaneum beetle, a Trichoplax adhaerens Placozoa, a Tubifex tubifex oligochaeta, a laboratory mouse, a Guinea pig, a Chicken, a Cat, a Dog, a Hamster, a Lamprey, a Medaka fish, a Rat, a Rhesus macaque, a Cotton rat, a Zebra finch, a Takifugu pufferfish, an African clawed frog, or a Zebrafish. In exemplary embodiments, a cell is a Saccharomyces cerevisiae yeast cell. In particularly exemplary embodiments, a cell is a Saccharomyces cerevisiae W303a yeast cell.
A cell of the invention may be derived from a tissue or from a cell line grown in tissue culture. A cell line may be adherent or non-adherent, or a cell line may be grown under conditions that encourage adherent, non-adherent or organotypic growth using standard techniques known to individuals skilled in the art. Cell lines and methods of culturing cell lines are known in the art. Non-limiting examples of cell lines commonly cultured in a laboratory may include HeLa, a cell line from the National Cancer Institute's 60 cancer cell lines, DU145 (prostate cancer), Lncap (prostate cancer), MCF-7 (breast cancer), MDA-MB-438 (breast cancer), PC3 (prostate cancer), T47D (breast cancer), THP-1 (acute myeloid leukemia), U87 (glioblastoma), SHSYSY Human neuroblastoma cells, Saos-2 cells (bone cancer), Vero, GH3 (pituitary tumor), PC12 (pheochromocytoma), MC3T3 (embryonic calvarium), Tobacco BY-2 cells, Zebrafish ZF4 and AB9 cells, Madin-Darby canine kidney (MDCK), or Xenopus A6 kidney epithelial cells.
As described in Section (I) above, two cell samples, or lysates derived from two cell samples are combined, and a tagged target chromatin of the invention is isolated from the combined cells or combined cell lysates. Typically, cells in two cell samples of the invention are from the same type of cells or they may be derived from the same type of cells. For instance, cells may comprise a heterologous nucleic acid in a target chromatin, and may also comprise a heterologous protein expressed in a cell of the invention. The heterologous nucleic acid in a target chromatin may be used for tagging a chromatin of the invention, and the heterologous protein expressed in a cell may be used for tagging a target chromatin as described in Section I(d). In some embodiments, cells in two cell samples of the invention are from the same type of cells. In other embodiments, cells in the first cell sample are derived from the same cell type as cells in the second cell sample.
Two cell samples of the invention may be from the same genus, species, variety or strain of cells. In preferred embodiments, two cell samples of the invention are Saccharomyces cerevisiae yeast cells or derivatives of Saccharomyces cerevisiae yeast cells. In exemplary embodiments, two cell samples of the invention are Saccharomyces cerevisiae W303a yeast cells or derivatives of Saccharomyces cerevisiae W303a yeast cells. In exemplary embodiments, two cell samples of the invention are derivatives of Saccharomyces cerevisiae W303a yeast cells comprising the lexA binding site upstream of the GAL1 transcription start site, wherein protein A is expressed in one of the cell samples of derived Saccharomyces cerevisiae W303a yeast cells.
According to the invention, a metabolically labeled cell sample and an unlabeled cell sample are combined to generate a combined cell sample, or lysates derived from the two cell samples are combined to generate a combined cell lysate. Cell samples may be combined in a weight to weight (w/w) ratio of about 1:100 to about 100:1, about 1:50 to about 50:1, about 1:25 to about 25:1, preferably about 1:10 to about 10:1, and more preferably about 1:5 to about 5:1. In preferred embodiments, cell samples are combined in a w/w ratio of about 1:5 to about 5:1, about 1:2 to about 2:1, about 1:1.5 to about 1.5:1, or about 1:1. In exemplary embodiments, cell samples are combined in a w/w ratio of about 1:1. If cell lysates derived from two cell samples of the invention are combined, lysates derived from cell ratios described herein are combined. Individuals of ordinary skill in the art will recognize that ratios of cell samples or lysates derived from cell samples described herein may be subject to statistical confidence limits of actual cell weight. For instance, the ratio may be based on 85, 90, 95% or more confidence limits on cell weight.
The number of cells in a cell sample can and will vary depending on the type of cells, the abundance of a target chromatin in a cell, and the method of protein identification used, among other variables. For instance, if a cell of the invention is Saccharomyces cerevisiae, about 5×1011 to about 5×1012, more preferably, about 1×1011 to about 1×1012 cells may be used in a cell sample. In some embodiments, about 1×1011 to about 1×1012 Saccharomyces cerevisiae cells are used in a cell sample.
Two cell samples of the invention are typically grown identically. Identically grown cell samples minimizes potential structural or functional differences at a target chromatin present in both cell samples. As used herein, “grown identically” refers to cultured cell samples grown using similar culture condition, or cells from a tissue harvested using identical harvesting techniques. As described below, the two cell samples of the invention are grown identically in a manner that allows the metabolic labeling of proteins in one of the cell samples. For instance, the two cell samples of the invention are grown identically, except that one of the cell samples may be grown in the presence of a labeled amino acid as described in the examples, to generate a cell sample with metabolically labeled proteins.
Proteins in a cell sample are metabolically labeled. Methods of metabolically labeling proteins in a cell are known in the art and may comprise culturing a cell in the presence of at least one labeled analogue of a biomolecule that is metabolized by a cell of the invention. When the labeled analog of a biomolecule is supplied to cells in culture instead of the unlabeled biomolecule, the labeled biomolecule is incorporated into all newly synthesized proteins. After a number of cell divisions, each instance of this particular labeled biomolecule will be replaced by its labeled analog. Since there is hardly any chemical difference between the labeled biomolecule and the unlabeled biomolecule, the cells behave exactly like the control cell population grown in the presence of unlabeled biomolecule. As such, up to 100% of the particular biomolecule in a cell may be labeled. In some embodiments, up to 10, 20, 30, 40, 50, 60, 70, 80, 90 or up to 100% of the particular biomolecule in a cell is labeled. In preferred embodiments, up to 50, 60, 70, 80, 90 or up to 100%, and more preferably up to 90 or up to 100% of the particular biomolecule in a cell is labeled. In preferred embodiments, up to 100% of the particular biomolecule in a cell is labeled.
A cell may be labeled by culturing a cell in the presence of one or more than one labeled biomolecule. For instance, a cell may be cultured in the presence of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more labeled biomolecules. In some embodiments, a cell may be cultured in the presence of 1, 2, 3, 4, or 5 labeled biomolecules. In other embodiments, a cell may be cultured in the presence of 5, 6, 7, 8, 9, or 10 labeled biomolecules. In preferred embodiments, a cell may be cultured in the presence of 1 or 2 labeled biomolecules.
Non-limiting examples of a biomolecule that may be labeled and is metabolized by a cell of the invention may include an amino acid, a nucleic acid, a carbohydrate or a labeled molecule that may be incorporated into an amino acid, a nucleic acid, or a carbohydrate. Non-limiting examples of a labeled molecule that may be incorporated into an amino acid, a nucleic acid, a carbohydrate may include labeled ammonium sulfate, and labeled ammonium chloride. A labeled biomolecule may be a component of a cell culture medium such as a food source, e.g., glucose, sera or cell extracts. In some embodiments, a labeled biomolecule that is metabolized by a cell of the invention is a labeled nucleic acid. In other embodiments, a labeled biomolecule that is metabolized by a cell of the invention is a labeled carbohydrate such as [13C]glucose.
In preferred embodiments, a biomolecule that is metabolized by a cell of the invention is a labeled amino acid. In general, a labeled amino acid of the invention may be a labeled L-amino acid, a labeled D-amino acid or a mixture thereof. In preferred embodiments, a labeled amino acids is a labeled L-amino acids. A labeled amino acid may be a free amino acid or an amino acid salt. A labeled amino acid may also be in the form of intact protein or peptide, provided that the protein or peptide comprises a labeled amino acid of the invention. In some preferred embodiments, a labeled amino acid that may be used for metabolically labeling a cell of the invention may be a labeled L-Lysine, L-Arginine, L-Methionine, L-Tyrosine, or combinations thereof.
A labeled biomolecule may be labeled using a heavy isotope of one or more atoms of the biomolecule. Non limiting examples of a heavy isotope of one or more atoms of a biomolecule may include heavy hydrogen, carbon, nitrogen, phosphorous, oxygen, or sulfur. A labeled biomolecule may be about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 18, 19 or 20Da or more heavier than an unlabeled biomolecule. In some embodiments, a labeled biomolecule is about 1, 2, 3, 4, or 5Da heavier than an unlabeled biomolecule. In other embodiments, a labeled biomolecule is about 5, 6, 7, 8, 9, or 10Da heavier than an unlabeled biomolecule. In yet other embodiments, a labeled biomolecule is about 10, 11, 12, 13, 14, or 15Da heavier than an unlabeled biomolecule. In additional embodiments, a labeled biomolecule is about 15, 16, 17 18, 19 or 20Da heavier than an unlabeled biomolecule. In preferred embodiments, a labeled biomolecule is about 4, 5, 6, 7, 8, 9, or 10Da heavier than an unlabeled biomolecule.
In preferred embodiments, a labeled biomolecule is a labeled amino acid that may be used for metabolically labeling a cell of the invention may be a heavy analog of L-Lysine, L-Arginine, L-Methionine, L-Tyrosine, or combinations thereof. Non limiting examples of heavy analogs of L-Lysine, L-Arginine, L-Methionine, L-Tyrosine may include, [13C6]-L-Lysine, [13C6, 15N2]-L-Lysine, [13C6, 15N2, D9]-L-Lysine, [15N2, D9]-L-Lysine, [4,4,5,5-D4]-L-Lysine, [15N2]-L-Lysine, [13C6, 15N2]-L-Lysine, [13C6]-L-Arginine, [U-13C6, 15N4]-L-Arginine, [U-13C6, 15N4, D7]-L-Arginine, [15N4, D7]-L-Arginine, [15N4]-L-Arginine, [13C6, 15N4]-L-Arginine, [1-13C, methyl-D3]-L-Methionine, [13C9; 9 Da]-L-Tyrosine, [15N]-L-Tyrosine, and [13C9, 15N]-L-Tyrosine. In an exemplary embodiment, a labeled amino acid used to metabolically label a cell of the invention is [13C6, 15N4]-L-Arginine.
(b) Chromatin
A method of the invention comprises identification of a protein and post-translational modification of a protein associated with a target chromatin. Generally, chromatin refers to the combination of nucleic acids and proteins in the nucleus of a eukaryotic cell. However, it is contemplated that the term “chromatin” may also refer to the combination of any nucleic acid sequence and proteins associated with the nucleic acid sequence in any cell.
A chromatin of the invention may comprise single stranded nucleic acid, double stranded nucleic acid, or a combination thereof. In some embodiments, a chromatin comprises single stranded nucleic acid. In other embodiments, a chromatin comprises a combination of single stranded and double stranded nucleic acids. In yet other embodiments, a chromatin comprises double stranded nucleic acid.
A chromatin of the invention may comprise a ribonucleic acid (RNA), a deoxyribonucleic acid (DNA), or a combination of RNA and DNA. In some embodiments, a chromatin of the invention comprises a combination of a RNA sequence and proteins associated with the RNA sequence in a cell. Non-limiting examples of RNA sequences may include mRNA, and non-coding RNA such as tRNA, rRNA, snoRNAs, microRNAs, siRNAs, piRNAs and the long noncoding RNA (IncRNA). In preferred embodiments, a chromatin of the invention comprises a combination of a DNA sequence and proteins associated with the DNA sequence in a cell. In other preferred embodiments, a chromatin of the invention comprises a combination of RNA and DNA sequences, and proteins associated with the RNA and DNA sequence in a cell. Non limiting examples of chromatin that may comprise a combination of RNA and DNA may include genomic DNA undergoing transcription, or genomic DNA comprising non-coding RNA such as IncRNA.
A chromatin of the invention may be genomic chromatin such as, chromatin from a chromosome of a cell, or chromatin from an organelle in the cell. Alternatively, a chromatin may be chromatin from an extrachromosomal nucleic acid sequence. In some embodiments, a chromatin of the invention is chromatin from an organelle in the cell. Non-limiting examples of a chromatin from an organelle may include mitochondrial nucleic acid sequence in plant and animal cells, and a chloroplast nucleic acid sequence in plant cells. In some embodiments, a nucleic acid sequence of the invention is a mitochondrial nucleic acid sequence. In other embodiments, a nucleic acid sequence of the invention is a chloroplast nucleic acid sequence.
In some embodiments, a chromatin of the invention is chromatin from an extrachromosomal nucleic acid sequence. The term “extrachromosomal,” as used herein, refers to any nucleic acid sequence not contained within the cell's genomic nucleic acid sequence. An extrachromosomal nucleic acid sequence may comprise some sequences that are identical or similar to genomic sequences in the cell, however, an extrachromosomal nucleic acid sequence as used herein does not integrate with genomic sequences of the cell. Non-limiting examples of an extrachromosomal nucleic acid sequence may include a plasmid, a virus, a cosmid, a phasmid, and a plasmid.
In some preferred embodiments, a chromatin of the invention is genomic chromatin. In exemplary embodiments, a chromatin of the invention is genomic chromatin of a eukaryotic cell. A eukaryotic cell of the invention may be as described in Section I(a) above.
Primary functions of genomic chromatin of a eukaryotic cell may be DNA packaging into a smaller volume to fit in the cell, strengthening of the DNA to allow mitosis, prevent DNA damage, and to control gene expression and DNA replication. As described above, genomic chromatin of a eukaryotic cell may comprise DNA sequences and a plurality of DNA-binding proteins as well as certain RNA sequences, assembled into higher order structural or functional regions. As used herein, a “structural or functional feature of a chromatin”, refers to a chromatin feature characterized by, or encoding, a function such as a regulatory function of a promoter, terminator, translation initiation, enhancer, etc., or a structural feature such as heterochromatin, euchromatin, a nucleosome, a telomere, or a centromere. A physical feature of a nucleic acid sequence may comprise a functional role and vice versa. As described below, a chromatin of the invention may be a chromatin fragment, and as such may comprise a fragment of a physical or functional feature of a chromatin, or no physical or functional features or known physical or functional features.
The primary protein components of genomic eukaryotic chromatin are histones that compact the DNA into a nucleosome. The nucleosome comprises an octet of histone proteins around which is wound a stretch of double stranded DNA sequence of about 150 to about 250 bp in length. Histones H2A, H2B, H3 and H4 are part of the nucleosome while histone H1 may act to link adjacent nucleosomes together into a higher order structure. Histones are subject to post translational which may affect their function in regulating chromatin function. Such modifications may include methylation, citrullination, acetylation, phosphorylation, SUMOylation, ubiquitination, and ADP-ribosylation.
Many further polypeptides and protein complexes interact with the nucleosome and the histones to regulate chromatin function. A “polypeptide complex” as used herein, is intended to describe proteins and polypeptides that assemble together to form a unitary association of factors. The members of a polypeptide complex may interact with each other via non-covalent or covalent bonds. Typically members of a polypeptide complex will cooperate to enable binding either to a nucleic acid sequence or to polypeptides and proteins already associated with or bound to a nucleic acid sequence in chromatin. Chromatin associated polypeptide complexes may comprise a plurality of proteins and/or polypeptides which each serve to interact with other polypeptides that may be permanently associated with the complex or which may associate transiently, dependent upon cellular conditions and position within the cell cycle. Hence, particular polypeptide complexes may vary in their constituent members at different stages of development, in response to varying physiological conditions or as a factor of the cell cycle. By way of example, in animals, polypeptide complexes with known chromatin remodelling activities include Polycomb group gene silencing complexes as well as Trithorax group gene activating complexes.
Additionally, a protein associated with a chromatin of the invention may be a protein normally expressed in a cell, or may be an exogenous heterologous protein expressed in a cell. In some embodiments, a protein associated with a chromatin of the invention is a protein normally expressed in a cell. In other embodiments, a protein associated with a chromatin of the invention is a protein normally expressed in a cell.
A chromatin of the invention may be an intact and complete chromatin from the cell, or may be a fragment of a chromatin in a cell. In some embodiments, a chromatin of the invention is an intact chromatin isolated from a cell. For instance, a chromatin of the invention may be a plasmid, a cosmid, or a phage chromatin or a complete organellar chromatin. In preferred embodiments, a chromatin of the invention is a fragment of a chromatin from a cell. In exemplary embodiments, a chromatin of the invention is a fragment of a genomic chromatin from a cell.
When a chromatin of the invention is a fragment of a chromatin in a cell, any method of fragmenting a chromatin known in the art may be used. Such methods may include physical methods of fragmenting a chromatin, or enzymatic digestion of a nucleic acid sequence of a chromatin. In some embodiments, a fragment of a chromatin may be generated using enzymatic digestion of a nucleic acid sequence in chromatin. Non-limiting examples of enzymatic digestion may include random or sequence specific enzymatic digestion using restriction enzymes, nucleases, combinations of restriction enzymes and nucleases, or combinations of nicking and other nucleases such as NEBNextTM fragmentase, which comprises a nicking enzyme that randomly generates nicks in double stranded DNA and another enzyme that cuts the strand opposite to the generated nicks.
In other embodiments, a fragment of a chromatin may be generated using a physical method of fragmenting a chromatin. Non-limiting examples of physical fragmenting methods that may be used to fragment a chromatin of the invention may include nebulization, sonication, and hydrodynamic shearing. In some embodiments, a fragment of a chromatin may be generated using nebulization. In other embodiments, a fragment of a chromatin may be generated using hydrodynamic shearing. In preferred embodiments, a fragment of a chromatin may be generated using sonication. During sonication, a sample comprising chromatin is subjected to ultrasonic waves, whose vibrations produce gaseous cavitations in the liquid that shear or break high molecular weight molecules such as chromatin through resonance vibration. Sonication methods that may be used to generate a chromatin of the invention are known in the art A fragment of a chromatin of the invention may comprise a nucleic acid sequence fragment and may be about 10, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100, 2150, 2200, 2250, 2300, 2350, 2400, 2450, 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850, 2900, 2950, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or about 10000 bases long or more. In some embodiments, a chromatin of the invention may comprise a nucleic acid sequence fragment of about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, or about 500 bases long. In other embodiments, a chromatin of the invention may comprise a nucleic acid sequence fragment of about 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, or about 1000 bases long. In yet other embodiments, a chromatin of the invention may comprise a nucleic acid sequence fragment of about 1000, 1010, 1020, 1030, 1040, 1050, 1060, 1070, 1080, 1090, 1100, 1110, 1120, 1130, 1140, 1150, 1160, 1170, 1180, 1190, 1200, 1210, 1220, 1230, 1240, 1250, 1260, 1270, 1280, 1290, 1300, 1310, 1320, 1330, 1340, 1350, 1360, 1370, 1380, 1390, 1400, 1410, 1420, 1430, 1440, 1450, 1460, 1470, 1480, 1490, or about 1500 bases long. In other embodiments, a chromatin of the invention may comprise a nucleic acid sequence fragment of about 1500, 1510, 1520, 1530, 1540, 1550, 1560, 1570, 1580, 1590, 1600, 1610, 1620, 1630, 1640, 1650, 1660, 1670, 1680, 1690, 1700, 1710, 1720, 1730, 1740, 1750, 1760, 1770, 1780, 1790, 1800, 1810, 1820, 1830, 1840, 1850, 1860, 1870, 1880, 1890, 1900, 1910, 1920, 1930, 1940, 1950, 1960, 1970, 1980, 1990, or about 2000 bases long. In additional embodiments, a chromatin of the invention may comprise a nucleic acid sequence fragment of about 2000, 2100, 2150, 2200, 2250, 2300, 2350, 2400, 2450, or about 2500 bases long. In other embodiments, a chromatin of the invention may comprise a nucleic acid sequence fragment of about 2000, 2050, 2100, 2150, 2200, 2250, 2300, 2350, 2400, 2450, or about 2500 bases long. In still other embodiments, a chromatin of the invention may comprise a nucleic acid sequence fragment of about 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850, 2900, 2950, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or about 10000 bases long or more.
In some preferred embodiments, a chromatin fragment of the invention may comprise a nucleic acid sequence fragment of about 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000, 1010, 1020, 1030, 1040, 1050, 1060, 1070, 1080, 1090, 1100, 1110, 1120, 1130, 1140, 1150, 1160, 1170, 1180, 1190, 1200, 1210, 1220, 1230, 1240, or about 1250 bases long. In a preferred embodiment, a chromatin of the invention may comprise a nucleic acid sequence fragment of about 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, or about 850 bases long. In another preferred embodiment, a chromatin of the invention may comprise a nucleic acid sequence fragment of about 950, 960, 970, 980, 990, 1000, 1010, 1020, 1030, 1040, or about 1050 bases long.
In other preferred embodiments, a chromatin fragment of the invention may comprise a nucleic acid sequence fragment of about 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000, 1010, 1020, 1030, 1040, 1050, 1060, 1070, 1080, 1090, 1100, 1110, 1120, 1130, 1140, 1150, 1160, 1170, 1180, 1190, 1200, 1210, 1220, 1230, 1240, 1250, 1260, 1270, 1280, 1290, 1300, 1310, 1320, 1330, 1340, 1350, 1360, 1370, 1380, 1390, 1400, 1410, 1420, 1430, 1440, 1450, 1460, 1470, 1480, 1490, or about 1500 bases long. In a preferred embodiment, a chromatin of the invention may comprise a nucleic acid sequence fragment of about 950, 960, 970, 980, 990, 1000, 1010, 1020, 1030, 1040, or about 1050 bases long. In another preferred embodiment, a chromatin of the invention may comprise a nucleic acid sequence fragment of about 1200, 1210, 1220, 1230, 1240, 1250, 1260, 1270, 1280, 1290, or about 1300 bases long.
As described in this section above, a chromatin of the invention may comprise one or more nucleosomes. As such, a chromatin fragment of the invention may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or about 20 nucleosomes. In some embodiments, a chromatin fragment of the invention may comprise about 1, 2, 3, 4, or about 5 nucleosomes. In other embodiments, a chromatin fragment of the invention may comprise about 5, 6, 7, 8, 9, or about 10 nucleosomes. In yet other embodiments, a chromatin fragment of the invention may comprise about 10, 11, 12, 13, 14, or about 15 nucleosomes. In other embodiments, a chromatin fragment of the invention may comprise about 15, 16, 17, 18, 19, or about 20 nucleosomes. In preferred embodiments, a chromatin fragment of the invention may comprise about 4 nucleosomes. In other preferred embodiments, a chromatin fragment of the invention may comprise about 5 nucleosomes.
A target chromatin fragment of the invention may comprise a structural or a functional feature of chromatin as described above, a fragment of a physical or functional feature, or no physical or functional features or known physical or functional features. In some embodiments, a target chromatin fragment of the invention comprises a structural feature of chromatin. In other embodiments, a target chromatin fragment of the invention comprises no physical or functional features or known physical or functional features. In yet other embodiments, a target chromatin fragment of the invention comprises a functional feature of chromatin. In exemplary embodiments, a functional feature of chromatin is a promoter. In particularly exemplary embodiments, a functional feature of chromatin is a GAL1 promoter of Saccharomyces cerevisiae. 
(c) Preparation of Cell Lysate
A target chromatin is isolated from a combined cell lysate. A combined cell lysate comprises a lysate of two combined cell samples, or a combination of two cell lysates derived from two cell samples, wherein a target chromatin is tagged in one of the cell samples. Irrespective of whether one cell sample or a combined cell sample is lysed, a skilled practitioner of the art will appreciate that structural and functional features of a target chromatin must be preserved during cell lysis and isolation of the target chromatin. The association of proteins with a target chromatin may be preserved during cell lysis and isolation of the target chromatin using methods known in the art for preserving a complex of proteins with a nucleic acid sequence. For instance, lysing of a cell and isolation of a target chromatin may be performed under refrigeration or using cryogenic methods and buffer conditions capable of preserving association of proteins and nucleic acid sequences. In addition, a complex of proteins with a nucleic acid may be preserved by crosslinking protein and nucleic acid complexes in a cell prior to lysing and isolating a chromatin. Crosslinking protein and nucleic acid complexes in a cell may also capture, or preserve, transient protein-protein and protein-nucleic acid interactions.
In some embodiments, a complex of proteins with a nucleic acid may be preserved by crosslinking protein and nucleic acid complexes in a chromatin prior to lysing a cell and isolating the chromatin. Crosslinking is the process of joining two or more molecules such as two proteins or a protein and a nucleic acid molecule, by a covalent bond. Molecules may be crosslinked by irradiation with ultraviolet light, or by using chemical crosslinking reagents. Chemical crosslinking reagents capable of crosslinking proteins and nucleic acids are known in the art and may include crosslinking reagents that target amines, sulfhydryls, carboxyls, carbonyls or hydroxyls; omobifunctional or heterobifunctional crosslinking reagent, variable spacer arm length or zero-length crosslinking reagents, cleavable or non-cleavable crosslinking reagents, and photoreactive crosslinking reagents. Non-limiting examples of crosslinking reagents that may be used to crosslink protein complexes and/or protein complexes and nucleic acids may include formaldehyde, glutaraldehyde, disuccinimidyl glutarate, disuccinimidyl suberate, a photoreactive amino acid such as photo-leucine or photo-methionine, and succinimidyl-diazirine. The degree of crosslinking can and will vary depending on the application of a method of the invention, and may be experimentally determined.
In a preferred embodiment, a complex of proteins with a nucleic acid in a chromatin of the invention may be preserved by crosslinking protein and nucleic acid complexes in a cell prior to lysing using formaldehyde. In an exemplary embodiment, a complex of proteins with a nucleic acid in a chromatin of the invention may be preserved by crosslinking protein and nucleic acid complexes in a cell prior to lysing using formaldehyde as described in the examples.
A skilled practitioner of the art will appreciate that protocols for lysing a cell can and will vary depending on the type of cell, the target chromatin of the invention, and the specific application of a method of the invention. Non limiting examples of methods that may be used to lyse a cell of the invention may include cell lysis using a detergent, an enzyme such as lysozyme, incubation in a hypotonic buffer which causes a cell to swell and burst, mechanical disruption such as liquid homogenization by forcing a cell through a narrow space, sonication, freeze/thaw, mortar and pestle, glass beads, and combinations thereof. In some embodiments, when a cell of the invention is a yeast cell, the cell may be cryogenically lysed under liquid nitrogen temperature with glass beads. In exemplary embodiments, when a cell of the invention is a yeast cell, the cell may be cryogenically lysed under liquid nitrogen temperature with glass beads as described in the examples.
Buffer conditions used during lysing and isolation of a chromatin of the invention can and will be altered to control stringent conditions during cell lysis and isolation to preserve association of proteins and nucleic acid sequences of a chromatin. “Stringent conditions” in the context of chromatin isolation are conditions capable of preserving specific association of proteins and nucleic acids of a chromatin, but minimizing non-specific association of proteins and nucleic acids. Stringent condition can and will vary depending on the application of a method of the invention, the target chromatin of the invention, the nucleic acid sequence in a target chromatin, the proteins or protein complexes associated with a target chromatin of the invention, whether or not proteins, protein complexes and nucleic acid sequences are crosslinked, and the conditions used for crosslinking proteins, protein complexes and nucleic acid sequences of a target chromatin. For instance, more stringent buffer conditions may be used in a method of the invention wherein proteins, protein-protein complexes, and protein-nucleic acid complexes are crosslinked compared to a method of the invention wherein proteins, protein-protein complexes, and protein-nucleic acid complexes are not crosslinked. As such, stringent buffer conditions used during cell lysis and isolation of a nucleic acid sequence of the invention may be experimentally determined for each application wherein a method of the invention is used. Buffer conditions that may alter stringent conditions during cell lysis and isolation may include pH and salt concentration. In preferred embodiments, proteins, protein-protein complexes, and protein-nucleic acid complexes of a target chromatin of the invention are crosslinked, and stringent buffer conditions are used during lysis and isolation of a chromatin of the invention. In exemplary embodiments, proteins, protein-protein complexes, and protein-nucleic acid complexes of a target chromatin of the invention are crosslinked, and stringent buffer conditions are used during lysis and isolation of a chromatin of the invention and are as described in the examples.
(d) Chromatin Isolation
According to the invention, a tagged target chromatin is isolated from a combined cell lysate. As described in Sections I(a) and I(c) above, a combined cell lysate comprises a lysate of two combined cell samples, or a combination of two cell lysates derived from two cell samples, wherein a target chromatin is tagged in one of the lysates, or one of the cell samples. As such, a target chromatin is isolated from a cell lysate comprising a combination of a tagged target chromatin and an untagged target chromatin. The ratio of tagged target chromatin to untagged target chromatin reflects the ratio at which the two cell samples or the lysates derived from the two cell sample are combined. In addition, proteins in one of the cell samples or lysate derived from one of the cell samples are metabolically labeled. Therefore, when a tagged target chromatin is from a cell sample wherein proteins are metabolically labeled, a cell lysate of the invention comprises a combination of a tagged target chromatin comprising metabolically labeled proteins, and an untagged target chromatin comprising unlabeled proteins. Conversely, when a tagged target chromatin is from a cell sample wherein proteins are unlabeled, a cell lysate of the invention comprises a combination of a tagged target chromatin comprising unlabeled proteins, and an untagged target chromatin comprising labeled proteins.
A target chromatin may be isolated from a mixture of chromatins or chromatin fragments in a cell lysate as described in this section. As used herein, a target nucleic acid sequence is said to be “isolated” or “purified” when it is substantially free of proteins not associated with the target chromatin, nucleic acid sequences other than the nucleic acid sequences associated with the target chromatin, and other cell debris and cell contents resulting from extraction and preparation of the target chromatin from a cell. A target chromatin of the present invention may be purified to homogeneity or other degrees of purity. In general, the level of purity of an isolated target chromatin can and will vary depending on the cell type, the specific chromatin to be isolated, and the intended use of a target chromatin of the invention. The level of purity of an isolated target chromatin may be determined using methods known in the art. For instance, the level of purity of an isolated target chromatin may be determined by determining the level of purity of a nucleic acid sequence associated with a target chromatin, by determining the level of purity of a protein associated with a target chromatin, or by determining the level of enrichment of a target chromatin, compared to a non-target chromatin in a cell. In preferred embodiments, the level of purity of an isolated target chromatin is determined by determining the level of enrichment of a target chromatin, compared to a non-target chromatin in a cell. Determining the level of enrichment of a target chromatin, compared to a non-target chromatin in a cell may be as described in this section below.
A target chromatin of the invention may be isolated using methods known in the art, such as electrophoresis, molecular, immunological and chromatographic techniques, ion exchange, hydrophobic, affinity, and reverse-phase HPLC chromatography, size exclusion chromatography, precipitation, dialysis, chromatofocusing, ultrafiltration and diafiltration techniques, and combinations thereof. For general guidance in suitable purification techniques, see Scopes, R., Protein Purification, Springer-Vertag, NY (1982).
In general, a method of the invention comprises isolating a target chromatin by affinity purification, or affinity purification in combination with other methods of isolating chromatin described above. In a preferred embodiment, a method of the invention comprises isolating a target chromatin by affinity purification. Non limiting examples of affinity purification techniques that may be used to isolate a target chromatin of the invention may include affinity chromatography, immunoaffinity chromatography, size exclusion chromatography, and combinations thereof. See, for example, Roe (ed), Protein Purification Techniques: A Practical Approach, Oxford University Press, 2nd edition, 2001.
In essence, affinity purification of a target chromatin may comprise tagging a target chromatin by contacting the target chromatin of the invention with a tag capable of specifically recognizing and binding one or more portions of a target chromatin. As described in Section (I), two cell samples, or lysates derived from the cell samples of the invention are combined, and a target chromatin in one of the cell samples or an extract from one of the cell samples is tagged. In addition, proteins in one cell sample, but not both of the cell samples are metabolically labeled. As such, a target chromatin may be tagged in a cell or an extract from a cell wherein proteins are metabolically labeled, and proteins specifically associated with an isolated target chromatin are metabolically labeled. Alternatively, a target chromatin may be tagged in a cell or an extract from a cell wherein proteins are not metabolically labeled, and proteins specifically associated with an isolated target chromatin are not metabolically labeled. In some embodiments, a target chromatin is tagged in a cell or an extract from a cell wherein proteins are metabolically labeled. In other embodiments, a target chromatin is tagged in a cell or an extract from a cell wherein proteins are metabolically labeled.
A tag may be capable of specifically recognizing and binding 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 components of a target chromatin. In preferred embodiments, a tag is capable of specifically recognizing and binding one component of a target chromatin.
A tag may be capable of specifically recognizing and binding a component in a target chromatin. A component in a target chromatin may be a nucleic acid sequence in a nucleic acid associated with a target chromatin, a protein associated with a target chromatin, or a chromatin structural or functional feature in a target chromatin. In some embodiments, a tag is capable of specifically recognizing and binding a protein associated with a target chromatin. In other embodiments, a tag is capable of specifically recognizing and binding a chromatin structural or functional feature in a target chromatin. In preferred embodiments, a tag is capable of specifically recognizing and binding a nucleic acid sequence associated with a target chromatin.
A nucleic acid sequence associated with a target chromatin that may be specifically recognized and bound by a tag of the invention may be a nucleic acid sequence normally found in a chromatin of a cell of the invention. Alternatively, a nucleic acid sequence associated with a target chromatin that may be specifically recognized and bound by a tag of the invention may be an exogenous nucleic acid sequence introduced into a cell to facilitate tagging a target chromatin of the invention. In some embodiments, a nucleic acid sequence that may be recognized and bound by a tag is a nucleic acid sequence normally found in a chromatin of a cell of the invention. In other embodiments, a nucleic acid sequence that may be recognized and bound by a tag of the invention is an exogenous nucleic acid sequence introduced into a cell of the invention to facilitate tagging a chromatin of the invention. Non limiting examples of an exogenous nucleic acid sequence introduced into a cell to facilitate tagging a target chromatin of the invention may be the lexA binding sequence, and the Lac operator. In a preferred embodiment, a heterologous nucleic acid sequence introduced into a cell to facilitate tagging a target nucleic acid sequence of the invention is the lexA binding sequence. In an exemplary embodiment, a heterologous nucleic acid sequence introduced into a cell to facilitate tagging a target nucleic acid sequence of the invention is the lexA binding sequence immediately upstream of the transcription start site.
Individuals of ordinary skill in the art will recognize that an exogenous chromatin component introduced into a cell to facilitate tagging a target chromatin of the invention cannot and will not disrupt a target chromatin, or a structural or functional feature of a target chromatin. Methods of designing a chromatin component and a tag capable of binding the chromatin component that do not disrupt a chromatin of the invention may depend on the particular application of a method of the invention, and may be determined experimentally. For instance, if an application of a method of the invention comprises promoter function, a tag may be designed to bind anywhere adjacent to the promoter, but without disrupting the promoter.
A tag of the invention may further comprise one or more affinity handles. As used herein, the term “affinity handle” may refer to any handle that may be bound by a substrate for affinity purification, as described below. A tag may comprise one or more than one affinity handle. The inclusion of more than one affinity handle in a tag of the invention may significantly increase the efficiency of affinity purification for a low copy number chromatin target. As such, a tag may further comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more affinity handles. In a preferred embodiment, a tag of the invention comprises one affinity handle.
Affinity handles may include any affinity handle for which a cognate binding agent is readily available. An affinity handle may be an aptamer, an antibody, an antibody fragment, a double-stranded DNA sequence, modified nucleic acids and nucleic acid mimics such as peptide nucleic acids, locked nucleic acids, phosphorodiamidate morpholino oligomers (PMO), a ligand, a ligand fragment, a receptor, a receptor fragment, a polypeptide, a peptide, a coenzyme, a coregulator, an allosteric molecule, non-immunoglobulin scaffolds such as Affibodies, Anticalins, designed Ankyrin repeat proteins and others, an ion, or a small molecule for which a cognate binding agent is readily available. The term “aptamer” refers to a polypeptide or a polynucleotide capable of binding to a target molecule at a specific region. It is generally accepted that an aptamer, which is specific in its binding to any polypeptide, may be synthesized and/or identified by in vitro evolution methods. Non limiting examples of handles that may be suitable for isolating a chromatin may include biotin or a biotin analogue such as desthiobiotin, digoxigenin, dinitrophenol or fluorescein, a macromolecule that binds to a nucleic acid or a nucleic acid binding protein such as the Lac repressor, a zinc finger protein, a transcription activator protein capable of binding a nucleic acid, or a transcription activator-like (TAL) protein, antigenic polypeptides such as protein A, or peptide ‘tags’ such as polyhistidine, FLAG, HA and Myc tags. In preferred embodiments, a tag of the invention comprises an antigenic polypeptide. In exemplary embodiments, a tag of the invention comprises the protein A antigenic polypeptide, or derivatives thereof. Protein A is capable of binding the lexA binding site, and comprises an affinity handle capapble of binding IgG. As such, protein A may be used as an affinity purification tag for purifying a target chromatin comprising a lexA binding tag.
In some embodiments, a tag of the invention is a nucleic acid tag capable of binding a nucleic acid sequence component of a chromatin, wherein the nucleic acid sequence component of the chromatin is introduced into a cell of the invention. In some embodiments, a tag of the invention is a nucleic acid tag capable of binding a nucleic acid sequence component of a chromatin, wherein the nucleic acid sequence component of the chromatin is normally present in a cell of the invention. Non-limiting examples of nucleic acid tags capable of binding a nucleic acid sequence component of a chromatin include antisense RNA or DNA nucleic acid tags, and tags comprising modified nucleic acids and nucleic acid mimics such as peptide nucleic acids, locked nucleic acids, phosphorodiamidate morpholino oligomers (PMO). In some embodiments, a tag of the invention is a nucleic acid tag comprising locked nucleotides. For instance, a nucleic acid tag comprising locked nucleotides may be as described in US20110262908 or US20120040857, and a peptide nucleic acid tag may be as described in Boffa et al. 1995 PNAS 92:1901-1905, the disclosures of all of which are incorporated herein in their entirety.
In some preferred embodiments, a tag of the invention is a protein tag capable of binding a nucleic acid sequence component of a chromatin, wherein the nucleic acid sequence component of the chromatin is a nucleic acid sequence normally found in a chromatin of a cell of the invention. Non limiting examples of a protein tag capable of binding a nucleic acid sequence normally found in a chromatin of a cell may be a nucleic acid binding protein such as protein A, the Lac repressor, a zinc finger protein, a transcription activator protein capable of binding a nucleic acid, or a transcription activator-like (TAL) protein. In one embodiment, a tag of the invention is a transcription activator protein capable of binding a nucleic acid sequence normally found in a chromatin of a cell of the invention. In another embodiment, a tag of the invention is a zinc finger protein capable of binding a nucleic acid sequence normally found in a chromatin of a cell of the invention. In yet another embodiment, a tag of the invention is a transcription activator-like (TAL) protein capable of binding a nucleic acid sequence normally found in a chromatin of a cell of the invention.
A nucleic acid binding protein tag of the invention may be a wild type nucleic acid binding protein capable of binding a nucleic acid sequence normally found in a target chromatin. Alternatively, a nucleic acid binding protein tag of the invention may be engineered to have binding specificity for a nucleic acid sequence component normally found in a target chromatin of the invention. Individuals of ordinary skill in the art will recognize that nucleic acid binding proteins such as zinc finger proteins, transcription activator proteins, and transcription activator-like (TAL) proteins may be engineered to have novel nucleic acid binding specificity compared to naturally-occurring forms of the proteins. See, for example, U.S. Pat. Nos. 6,453,242 and 6,534,261, and U.S. Pate. Appl. Nos 20110239315, 20120110685, and 20120270273, the disclosures of which are incorporated by reference herein in their entireties. In some embodiments, a nucleic acid binding protein tag of the invention is a wild type nucleic acid binding protein capable of binding a nucleic acid sequence normally found in a target chromatin. In other embodiments, a nucleic acid binding protein tag of the invention is a nucleic acid binding protein engineered to have binding specificity for a nucleic acid sequence component of a target chromatin of the invention. In a preferred embodiment, a nucleic acid binding protein tag of the invention is a zinc finger protein engineered to have binding specificity for a nucleic acid sequence component of a target chromatin of the invention. In another preferred embodiment, a nucleic acid binding protein tag of the invention is a TAL protein engineered to have binding specificity for a nucleic acid sequence component of a target chromatin of the invention.
In other preferred embodiments, a tag of the invention is a protein tag capable of binding a nucleic acid sequence component of a chromatin, wherein the nucleic acid sequence component of the chromatin is an exogenous nucleic acid sequence introduced into a cell of the invention. In exemplary embodiments, a tag of the invention is a protein A tag capable of binding the lexA exogenous nucleic acid sequence introduced in a cell of the invention. In an exemplary embodiment, a tag of the invention is a protein A tag capable of binding the lexA exogenous nucleic acid sequence introduced upstream of the transcriptional start site of the GAL1 promoter of a S. cereviseae cell as described in the examples.
A target chromatin may be contacted with a tag at any time during a method of the invention leading to isolation of target chromatin. For instance, a target chromatin may be contacted with a protein tag during cell culture by expressing the protein tag in a cell of the invention. Alternatively, a target chromatin may be contacted with a tag after cell culture but before cell lysis, after cell lysis, or after fragmentation of chromatin to generate chromatin fragments comprising a target chromatin.
In some embodiments, a target chromatin is contacted with a tag after cell culture but before cell lysis. As such, a tag may be introduced into a cell before cell lysis. Methods of introducing a tag into a cell of the invention can and will vary depending on the type of cell, the tag, and the application of a method of the invention. For instance, a nucleic acid tag may be electroporated into a cell after culture. In other embodiments, a target chromatin is contacted with a tag after cell lysis. In yet other embodiments, a target chromatin is contacted with a tag after cell lysis and chromatin fragmentation. In preferred embodiments, a target chromatin is contacted with a tag during cell culture by expressing the tag in a cell of the invention during cell culture. In exemplary embodiments, a target chromatin comprises the lexA binding site, and the lexA binding site is contacted with a protein A tag during cell culture by expressing the protein A in a cell of the invention during cell culture. In an exemplary embodiment, a target chromatin comprises the lexA binding site, and the lexA binding site is contacted with a protein A tag during cell culture by expressing the protein A in a yeast cell of the invention during cell culture as described in the examples.
A target chromatin contacted and bound by a tag as described above may be isolated using an affinity handle of the tag. The term “isolated”, may be used herein to describe a purified preparation of a target chromatin that is enriched for the target chromatin, but wherein the target chromatin is not necessarily in a pure form. That is, an isolated target chromatin is not necessarily 100% pure, but may be about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% pure. An isolated target chromatin may be enriched for the target chromatin, relative to a chromatin in the lysed preparation that was not contacted by a tag of the invention. An isolated target chromatin may be enriched by 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 fold relative to a chromatin that is not contacted by a tag of the invention. In some embodiments, an isolated target chromatin is enriched by 2, 3, 4, or 5 fold relative to a chromatin that was not contacted by a tag of the invention. In other embodiments, an isolated target chromatin is enriched by 5, 6, 7, 8, 9, or 10 fold relative to a chromatin that was not contacted by a tag of the invention. In an exemplary embodiment, an isolated target chromatin is enriched 4, 5, or 6 fold relative to a chromatin that was not contacted by a tag of the invention.
A target chromatin contacted and bound by a tag as described above may be isolated using any affinity purification method known in the art. In short, a tagged target chromatin is bound to a substrate capable of binding the affinity handle. The substrate comprising a bound target chromatin may then be washed to remove non-target chromatin and other cell debris, and the target chromatin may be released from substrate. Methods of affinity purification of material comprising an affinity handle are known in the art and may include binding the affinity handle to a substrate capable of binding the affinity handle. The substrate may be a gel matrix such as gel beads, the surface of a container, or a chip. The tagged target chromatin bound to the substrate may then be purified. Methods of purifying tagged molecules are known in the art and will vary depending on the target molecule, the tag, and the substrate. For instance, if the tag is a protein A tag bound to a lexA binding site in a target chromatin, the target chromatin may be bound to a magnetic bead substrate comprising IgG, and purified using a magnet.
(e) Protein Extraction, Identification, and Determination of Labeling
Proteins and peptides associated with an isolated target chromatin are extracted from the isolated target chromatin. Methods of extracting proteins from chromatin are generally known in the art of protein biochemistry. Generally, any extraction protocol suitable for isolating proteins and known to those of skill in the art may be used. Extracted proteins may also be further purified before protein identification. For instance, protein extracts may be further purified by differential precipitation, differential solubilization, ultracentrifugation, using chromatographic methods such as size exclusion chromatography, hydrophobic interaction chromatography, ion exchange chromatography, affinity chromatography, metal binding, immunoaffinity chromatography, HPLC, or gel electrophoriesis such as SDS-PAGE and QPNC-PAGE. In a preferred embodiment, extracted proteins are further purified using SDS-PAGE.
Extracted and purified intact proteins and post-translational modification of proteins may then be identified. Alternatively, extracted and purified intact proteins may be further digested, and the resulting peptide fragments are identified. In some embodiments, intact extracted proteins are identified. In preferred embodiments, extracted proteins are further digested, and the resulting peptide fragments are identified. For instance, protein extracts may be fragmented by enzymatically digesting the proteins using a protease such as trypsin. In exemplary embodiments, extracted proteins are further digested as described in the examples.
Methods of identifying proteins or protein fragments are known in the art and may include mass spectrometry (MS) analysis, or a combination of mass spectrometry with a chromatographic technique. Non limiting examples of mass spectrometer techniques may include tandem mass spectrometry (MS/MS), matrix-assisted laser desorption/ionization source with a time-of-flight mass analyzer (MALDI-TOF), inductively coupled plasma-mass spectrometry (ICP-MS), accelerator mass spectrometry (AMS), thermal ionization-mass spectrometry (TIMS), isotope ratio mass spectrometry (IRMS), and spark source mass spectrometry (SSMS). Chromatographic techniques that may be used with MS may include gas chromatography, liquid chromatography, and ion mobility spectrometry. In a preferred embodiment, proteins may be identified using tandem mass spectrometry in combination with liquid chromatography (LC-MS/MS). In another preferred embodiment, post-translational modification of proteins may be identified using tandem mass spectrometry in combination with liquid chromatography (LC-MS/MS).
As described above, proteins isolated with a chromatin of the invention may be labeled, unlabeled or a combination of labeled and unlabeled proteins. As described in Section I(d), if a target chromatin is tagged in a cell or an extract from a cell wherein proteins are metabolically labeled, proteins specifically associated with an isolated target chromatin are metabolically labeled, whereas unlabeled proteins, or proteins comprising a combination of labeled and unlabeled proteins are not specifically associated with the target chromatin. Alternatively, if a target chromatin may be tagged in a cell or an extract from a cell wherein proteins are not metabolically labeled, proteins specifically associated with an isolated target chromatin are metabolically labeled, whereas unlabeled proteins, or proteins comprising a combination of labeled and unlabeled proteins are not specifically associated with the target chromatin.
When an isolated and identified protein is a combination of labeled and unlabeled protein, the ratio of labeled to unlabeled protein may reflect a ratio at which a metabolically labeled cell sample and an unlabeled cell sample are combined to generate a combined cell sample, or lysates derived from the two cell samples are combined to generate a combined cell lysate. For instance, if a metabolically labeled cell sample and an unlabeled cell sample, or lysates derived from the two cell samples, are combined at a ratio of 1:1, the ratio of labeled to unlabeled isolated protein may be 1:1.
However, since the ratio of labeled to unlabeled isolated protein depends on the rate of exchange of the identified protein during extraction and processing of a cell sample, a ratio of labeled to unlabeled isolated protein may differ from the ratio at which a metabolically labeled cell sample and an unlabeled cell sample are combined to generate a combined cell sample, or lysates derived from the two cell samples are combined to generate a combined cell lysate. For example, if a metabolically labeled cell sample and an unlabeled cell sample, or lysates derived from the two cell samples, are combined at a ratio of 1:1, a ratio of labeled to unlabeled isolated protein may deviate from a ratio of 1:1. As such, a ratio of labeled to unlabeled isolated protein may be compared to a baseline for non-specifically associated proteins. For instance, a baseline for non-specifically associated proteins may be a ratio of labeled to unlabeled of one or more proteins in a combined lysate, wherein the one or more proteins are not associated with a chromatin. Non-limiting examples of proteins not associated with a chromatin may include enzymes required for metabolism, receptors, and ribosomoal proteins. In preferred embodiments, proteins not associated with a chromatin are ribosomal proteins, and a baseline for non-specifically associated proteins is a ratio of a labeled to unlabeled ribosomal protein, or an average of ratios of labeled to unlabeled ribosomal proteins. In a preferred embodiment, proteins not associated with a chromatin are 20 ribosomal proteins, and a baseline for non-specifically associated proteins is an average of ratios of the 20 labeled to unlabeled ribosomal proteins.
Isolated proteins with a ratio of labeled to unlabeled isolated protein may be specifically associated with a chromatin if the ratio of labeled to unlabeled isolated protein is significantly different from a baseline ratio. A significantly different ratio may be a ratio of labeled to unlabeled isolated protein greater than about 1, 2, 3, 4, 5, or more standard deviations than a baseline ratio. In some embodiments, a significantly different ratio is a ratio of labeled to unlabeled isolated protein greater than about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, or more standard deviations than a baseline ratio. In other embodiments, a significantly different ratio is a ratio of labeled to unlabeled isolated protein greater than about 1, 1.5, 2, or about 2.5 standard deviations than a baseline ratio. In preferred embodiments, a significantly different ratio is a ratio of labeled to unlabeled isolated protein greater than about 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9 or about 3 standard deviations than a baseline ratio. In exemplary embodiments, a significantly different ratio is a ratio of labeled to unlabeled isolated protein greater than about 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, or about 2.5 standard deviations than a baseline ratio.
Methods of determining if a protein or a protein fragment is labeled can and will vary depending on the type of label. For instance, if a protein is labeled using a tag, labeling may be determined using methods designed to detect the tag. For example, determining if a protein comprising a his-tag is tagged, untagged, or a combination of tagged and untagged may be by detecting the proteins comprising the his tag. If a protein is labeled using a radioactive isotope, labeling may be determined by determining the degree of radioactivity of isolated proteins or protein fragments. Alternatively, if a protein is labeled using a heavy isotope, MS analysis may be used to determine if a protein or a protein fragment is labeled or unlabeled. Advantageously, when a protein is labeled using a heavy isotope, MS analysis may be used to identify a protein or a protein fragment as described above, and to derive the MS data to determine if a protein or a protein fragment is labeled, unlabeled, or a combination of labeled and unlabeled protein or protein fragment.
In preferred embodiments, a protein is labeled using a heavy isotope, and MS analysis is used to identify a protein or a protein fragment, and to determine if a protein or a protein fragment is labeled, unlabeled, or a combination of labeled and unlabeled protein or protein fragment. Methods of deriving MS data to determine if a protein or a protein fragment is labeled, unlabeled, or a combination of labeled and unlabeled protein or protein fragment are known in the art, and may include using known computational techniques to distill MS data such as Mascot Distiller, Rosetta Elucidator, and MaxQuant. In some embodiments, MS data is derived using Rosetta Elucidator. In other embodiments, MS data is derived using MaxQuant. In preferred embodiments, MS data is derived using Mascot Distiller.
(f) Applications
A method of the invention may be used for any application wherein a determination of chromatin structure or function may be required. For instance, a method of the invention may be used to determine rearrangement in chromatin structure, genome metabolism, epigenetic regulatory mechanisms, transient association of proteins with chromatin, initiation or silencing of expression of a nucleic acid sequence, identify proteins transiently associated with a chromatin, or post-translational modification of proteins associated with a chromatin or chromatin rearrangement. An application of a method of the invention may include determining changes in chromatin function and structure in response to changing growth conditions, exposure to a drug or small molecule, or during stages of cell cycles.
In some embodiments, a method of the invention is used to determine differences in chromatin structure and function between a transcriptionally silent and a transcriptionally active state of a genomic locus. As such, proteins specifically associated with a genomic locus, and post-translational modifications of proteins associated with a chromatin comprising the genomic locus may be determined in cells comprising a transcriptionally silent state of a genomic locus, and in cells comprising a transcriptionally active state of a genomic locus. In preferred embodiments, a method of the invention is used to determine differences in chromatin structure and function between a transcriptionally silent and a transcriptionally active state of a Saccharomyces cerevisiae GAL1 genomic locus.
II. Method of TAL-ChAP-MS
In some aspects, the invention provides methods of isolating and identifying proteins specifically associated with a target chromatin. As described in Example 4 and FIG. 7, a method of the invention comprises isolating a target chromatin from a cell. As used herein, a “target chromatin” refers to a specific chromatin or a chromatin fragment that may be used in an application of the invention. According to the method, isolating the target chromatin isolates nucleic acid sequences and proteins, including proteins comprising posttranslational modifications, associated with the target chromatin. The proteins and posttranslational modifications of proteins associated with the target chromatin may then be identified, and a determination of which of the identified proteins and posttranslational modifications of proteins associated with a target chromatin isolated from a cell are specifically or non-specifically associated with the target chromatin is made.
To determine which of the identified proteins and posttranslational modifications of proteins associated with a target chromatin isolated from a cell are specifically or non-specifically associated with the target chromatin, a method of high-resolution mass spectrometry coupled with label-free proteomics was used. One with skill in the art will appreciate that label-free quantitative proteomics methods include the following fundamental steps: (i) sample preparation including protein extraction, reduction, alkylation, and digestion; (ii) sample separation by liquid chromatography (LC or LC/LC) and analysis by MS/MS; (iii) data analysis including peptide/protein identification, quantification, and statistical analysis. A method of the invention provides two cell samples, or lysates derived from two cell samples, comprising the target chromatin, wherein the target chromatin in one cell sample, but not both of the cell samples is tagged. With label-free quantitiative methods, each sample is separately prepared, then subjected to individual LC-MS/MS or LC/LC-MS/MS runs. As reviewed in Zhu et al., J Biomed Biotechnol 2010, and incorporated by reference herein, protein quantification is generally based on two categories of measurements. In the first are the measurements of ion intensity changes such as peptide peak areas or peak heights in chromatography. The second is based on spectral counting of identified proteins after MS/MS analysis. Peptide peak intensity or spectral count is measured for individual LC-MS/MS or LC/LC-MS/MS runs and changes in protein abundance are calculated via a direct comparison between different analyses.
In the present invention, the method of spectral counting is used to categorize whether proteins enriched with a section of chromatin are specific or contaminant. As such, determining the abundance of an identified protein in a tagged chromatin sample compared to the same protein in an untagged chromatin sample, may determine if the protein was specifically associated with the target chromatin of the invention. If a protein associated with a target chromatin is enriched in a tagged chromatin sample compared to the same protein in an untagged chromatin sample, then the protein is specifically associated with the target chromatin. If an identified protein is not enriched in a tagged chromatin sample compared to an untagged chromatin sample, then association of that protein with the target chromatin is not specific.
In the present invention, to measure enrichment of a protein, the normalized spectral abundance factor (NSAF) is calculated for each protein in each lane of an SDS-PAGE gel by dividing the number of spectral counts (normalized for the size of the protein) of a given protein by the sum of all normalized spectral counts of all proteins in the gel lane. The enrichment level for each protein is identified by calculating the fold enrichment (tagged chromatin/untagged chromatin) using the NSAF values.
(a) Cells
A target nucleic acid sequence may be isolated from any cell comprising the target nucleic acid sequence of the invention. A cell may be an archaebacterium, a eubacterium, or a eukaryotic cell. For instance, a cell of the invention may be a methanogen, a halophile or a thermoacidophile archaeabacterium, a gram positive, a gram negative, a cyanobacterium, a spirochaete, or a firmicute bacterium, a fungal cell, a moss cell, a plant cell, an animal cell, or a protist cell.
In some embodiments, a cell of the invention is a cell from an animal. A cell from an animal cell may be a cell from an embryo, a juvenile, or an adult. Suitable animals include vertebrates such as mammals, birds, reptiles, amphibians, and fish. Examples of suitable mammals include without limit rodents, companion animals, livestock, and primates. Non-limiting examples of rodents include mice, rats, hamsters, gerbils, and guinea pigs. Suitable companion animals include but are not limited to cats, dogs, rabbits, hedgehogs, and ferrets. Non-limiting examples of livestock include horses, goats, sheep, swine, cattle, llamas, and alpacas. Suitable primates include but are not limited to humans, capuchin monkeys, chimpanzees, lemurs, macaques, marmosets, tamarins, spider monkeys, squirrel monkeys, and vervet monkeys. Non-limiting examples of birds include chickens, turkeys, ducks, and geese. In some embodiments, a cell is a cell from a human.
In some embodiments, a cell may be from a model organism commonly used in laboratory research. For instance, a cell of the invention may be an E. coli, a Bacillus subtilis, a Caulobacter crescentus, a Mycoplasma genitalium, an Aliivibrio fischeri, a Synechocystis, or a Pseudomonas fluorescens bacterial cell; a Chlamydomonas reinhardtii, a Dictyostelium discoideum, a Tetrahymena thermophila, an Emiliania huxleyi, or a Thalassiosira pseudonana protist cell; an Ashbya gossypii, an Aspergillus nidulans, a Coprinus cinereus, a Cunninghamella elegans, a Neurospora crassa, a Saccharomyces cerevisiae, a Schizophyllum commune, a Schizosaccharomyces pombe, or an Ustilago maydis fungal cell; an Arabidopsis thaliana, a Selaginella moellendorffii, a Brachypodium distachyon, a Lotus japonicus, a Lemna gibba, a Zea mays, a Medicago truncatula, a Mimulus, a tobacco, a rice, a Populus, or a Nicotiana benthamiana plant cell; a Physcomitrella patens moss; an Amphimedon queenslandica sponge, an Arbacia punctulata sea urchin, an Aplysia sea slug, a Branchiostoma floridae deuterostome, a Caenorhabditis elegans nematode, a Ciona intestinalis sea squirt, a Daphnia spp. crustacean, a Drosophila fruit fly, a Euprymna scolopes squid, a Hydra Cnidarian, a Loligo pealei squid, a Macrostomum lignano flatworm, a Mnemiopsis leidyicomb jelly, a Nematostella vectensis sea anemone, an Oikopleura dioica free-swimming tunicate, an Oscarella carmela sponge, a Parhyale hawaiensis crustacean, a Platynereis dumerilii marine polychaetous annelid, a Pristionchus pacificus roundworm, a Schmidtea mediterranea freshwater planarian, a Stomatogastric ganglion of various arthropod species, a Strongylocentrotus purpuratus sea urchin, a Symsagittifera roscoffensis flatworm, a Tribolium castaneum beetle, a Trichoplax adhaerens Placozoa, a Tubifex tubifex oligochaeta, a laboratory mouse, a Guinea pig, a Chicken, a Cat, a Dog, a Hamster, a Lamprey, a Medaka fish, a Rat, a Rhesus macaque, a Cotton rat, a Zebra finch, a Takifugu pufferfish, an African clawed frog, or a Zebrafish. In exemplary embodiments, a cell is a Saccharomyces cerevisiae yeast cell. In particularly exemplary embodiments, a cell is a Saccharomyces cerevisiae W303a yeast cell.
A cell of the invention may be derived from a tissue or from a cell line grown in tissue culture. A cell line may be adherent or non-adherent, or a cell line may be grown under conditions that encourage adherent, non-adherent or organotypic growth using standard techniques known to individuals skilled in the art. Cell lines and methods of culturing cell lines are known in the art. Non-limiting examples of cell lines commonly cultured in a laboratory may include HeLa, a cell line from the National Cancer Institute's 60 cancer cell lines, DU145 (prostate cancer), Lncap (prostate cancer), MCF-7 (breast cancer), MDA-MB-438 (breast cancer), PC3 (prostate cancer), T47D (breast cancer), THP-1 (acute myeloid leukemia), U87 (glioblastoma), SHSYSY Human neuroblastoma cells, Saos-2 cells (bone cancer), Vero, GH3 (pituitary tumor), PC12 (pheochromocytoma), MC3T3 (embryonic calvarium), Tobacco BY-2 cells, Zebrafish ZF4 and AB9 cells, Madin-Darby canine kidney (MDCK), or Xenopus A6 kidney epithelial cells.
As described in Section (II) above, two cell samples, or lysates derived from two cell samples may be subjected to mass-spectrometry coupled with label-free proteomics, one sample of which contains a tagged target chromatin of the invention. Typically, cells in two cell samples of the invention are from the same type of cells or they may be derived from the same type of cells. For instance, cells may comprise a heterologous protein expressed in a cell of the invention. The heterologous protein expressed in a cell may be used for tagging a target chromatin as described in Section II(d). In some embodiments, cells in two cell samples of the invention are from the same type of cells. In other embodiments, cells in the first cell sample are derived from the same cell type as cells in the second cell sample.
Two cell samples of the invention may be from the same genus, species, variety or strain of cells. In preferred embodiments, two cell samples of the invention are Saccharomyces cerevisiae yeast cells or derivatives of Saccharomyces cerevisiae yeast cells. In exemplary embodiments, two cell samples of the invention are Saccharomyces cerevisiae W303a yeast cells or derivatives of Saccharomyces cerevisiae W303a yeast cells. In exemplary embodiments, two cell samples of the invention are derivatives of Saccharomyces cerevisiae W303a yeast cells, wherein protein A tagged transcription activator-like (TAL) protein engineered to bind upstream of the GAL1 transcription start site is expressed in one of the cell samples of derived Saccharomyces cerevisiae W303a yeast cells.
The number of cells in a cell sample can and will vary depending on the type of cells, the abundance of a target chromatin in a cell, and the method of protein identification used, among other variables. For instance, if a cell of the invention is Saccharomyces cerevisiae, about 5×1011 to about 5×1012, more preferably, about 1×1011 to about 1×1012 cells may be used in a cell sample. In some embodiments, about 1×1011 to about 1×1012 Saccharomyces cerevisiae cells are used in a cell sample.
Two cell samples of the invention are typically grown identically. Identically grown cell samples minimizes potential structural or functional differences at a target chromatin present in both cell samples. As used herein, “grown identically” refers to cultured cell samples grown using similar culture condition, or cells from a tissue harvested using identical harvesting techniques.
(b) Chromatin
A method of the invention comprises identification of a protein and post-translational modification of a protein associated with a target chromatin. Generally, chromatin refers to the combination of nucleic acids and proteins in the nucleus of a eukaryotic cell. However, it is contemplated that the term “chromatin” may also refer to the combination of any nucleic acid sequence and proteins associated with the nucleic acid sequence in any cell.
Chromatin of the invention may be as described in Section I(b) above.
(c) Preparation of Cell Lysate
A target chromatin is isolated from a cell lysate derived from a cell sample, wherein a target chromatin is tagged in the cell sample. The method of isolating a target chromatin is also performed on a cell lysate derived from a cell sample, wherein a target chromatin is untagged in the cell sample. A skilled practitioner of the art will appreciate that structural and functional features of a target chromatin must be preserved during cell lysis and isolation of the target chromatin. The association of proteins with a target chromatin may be preserved during cell lysis and isolation of the target chromatin using methods known in the art for preserving a complex of proteins with a nucleic acid sequence. For instance, lysing of a cell and isolation of a target chromatin may be performed under refrigeration or using cryogenic methods and buffer conditions capable of preserving association of proteins and nucleic acid sequences. In addition, a complex of proteins with a nucleic acid may be preserved by crosslinking protein and nucleic acid complexes in a cell prior to lysing and isolating a chromatin. Crosslinking protein and nucleic acid complexes in a cell may also capture, or preserve, transient protein-protein and protein-nucleic acid interactions.
In some embodiments, a complex of proteins with a nucleic acid may be preserved by crosslinking protein and nucleic acid complexes in a chromatin prior to lysing a cell and isolating the chromatin. Crosslinking is the process of joining two or more molecules such as two proteins or a protein and a nucleic acid molecule, by a covalent bond. Molecules may be crosslinked by irradiation with ultraviolet light, or by using chemical crosslinking reagents. Chemical crosslinking reagents capable of crosslinking proteins and nucleic acids are known in the art and may include crosslinking reagents that target amines, sulfhydryls, carboxyls, carbonyls or hydroxyls; omobifunctional or heterobifunctional crosslinking reagent, variable spacer arm length or zero-length crosslinking reagents, cleavable or non-cleavable crosslinking reagents, and photoreactive crosslinking reagents. Non-limiting examples of crosslinking reagents that may be used to crosslink protein complexes and/or protein complexes and nucleic acids may include formaldehyde, glutaraldehyde, disuccinimidyl glutarate, disuccinimidyl suberate, a photoreactive amino acid such as photo-leucine or photo-methionine, and succinimidyl-diazirine. The degree of crosslinking can and will vary depending on the application of a method of the invention, and may be experimentally determined.
In a preferred embodiment, a complex of proteins with a nucleic acid in a chromatin of the invention may be preserved by crosslinking protein and nucleic acid complexes in a cell prior to lysing using formaldehyde. In an exemplary embodiment, a complex of proteins with a nucleic acid in a chromatin of the invention may be preserved by crosslinking protein and nucleic acid complexes in a cell prior to lysing using formaldehyde as described in the examples.
A skilled practitioner of the art will appreciate that protocols for lysing a cell can and will vary depending on the type of cell, the target chromatin of the invention, and the specific application of a method of the invention. Non limiting examples of methods that may be used to lyse a cell of the invention may include cell lysis using a detergent, an enzyme such as lysozyme, incubation in a hypotonic buffer which causes a cell to swell and burst, mechanical disruption such as liquid homogenization by forcing a cell through a narrow space, sonication, freeze/thaw, mortar and pestle, glass beads, and combinations thereof. In some embodiments, when a cell of the invention is a yeast cell, the cell may be cryogenically lysed under liquid nitrogen temperature with glass beads. In exemplary embodiments, when a cell of the invention is a yeast cell, the cell may be cryogenically lysed under liquid nitrogen temperature with glass beads as described in the examples.
Buffer conditions used during lysing and isolation of a chromatin of the invention can and will be altered to control stringent conditions during cell lysis and isolation to preserve association of proteins and nucleic acid sequences of a chromatin. “Stringent conditions” in the context of chromatin isolation are conditions capable of preserving specific association of proteins and nucleic acids of a chromatin, but minimizing non-specific association of proteins and nucleic acids. Stringent condition can and will vary depending on the application of a method of the invention, the target chromatin of the invention, the nucleic acid sequence in a target chromatin, the proteins or protein complexes associated with a target chromatin of the invention, whether or not proteins, protein complexes and nucleic acid sequences are crosslinked, and the conditions used for crosslinking proteins, protein complexes and nucleic acid sequences of a target chromatin. For instance, more stringent buffer conditions may be used in a method of the invention wherein proteins, protein-protein complexes, and protein-nucleic acid complexes are crosslinked compared to a method of the invention wherein proteins, protein-protein complexes, and protein-nucleic acid complexes are not crosslinked. As such, stringent buffer conditions used during cell lysis and isolation of a nucleic acid sequence of the invention may be experimentally determined for each application wherein a method of the invention is used. Buffer conditions that may alter stringent conditions during cell lysis and isolation may include pH and salt concentration. In preferred embodiments, proteins, protein-protein complexes, and protein-nucleic acid complexes of a target chromatin of the invention are crosslinked, and stringent buffer conditions are used during lysis and isolation of a chromatin of the invention. In exemplary embodiments, proteins, protein-protein complexes, and protein-nucleic acid complexes of a target chromatin of the invention are crosslinked, and stringent buffer conditions are used during lysis and isolation of a chromatin of the invention and are as described in the examples.
(d) Chromatin Isolation
According to the invention, the method of isolating a target chromatin is performed on cell lysates derived from cell samples, wherein one sample comprises a target chromatin that is tagged in the cell sample and one sample comprises a target chromatin that is untagged in the cell sample. As described in Sections II(a) and II(c) above, a cell lysate comprises a lysate of a cell sample, wherein a target chromatin is tagged in one of the lysates, or one of the cell samples. A cell lysate also comprises a lysate of a cell sample, wherein a target chromatin is not tagged in one of the lysates, or one of the cell samples.
A target chromatin may be isolated from a mixture of chromatins or chromatin fragments in a cell lysate as described in this section. As used herein, a target nucleic acid sequence is said to be “isolated” or “purified” when it is substantially free of proteins not associated with the target chromatin, nucleic acid sequences other than the nucleic acid sequences associated with the target chromatin, and other cell debris and cell contents resulting from extraction and preparation of the target chromatin from a cell. A target chromatin of the present invention may be purified to homogeneity or other degrees of purity. In general, the level of purity of an isolated target chromatin can and will vary depending on the cell type, the specific chromatin to be isolated, and the intended use of a target chromatin of the invention. The level of purity of an isolated target chromatin may be determined using methods known in the art. For instance, the level of purity of an isolated target chromatin may be determined by determining the level of purity of a nucleic acid sequence associated with a target chromatin, by determining the level of purity of a protein associated with a target chromatin, or by determining the level of enrichment of a target chromatin, compared to a non-target chromatin in a cell. In preferred embodiments, the level of purity of an isolated target chromatin is determined by determining the level of enrichment of a target chromatin, compared to a non-target chromatin in a cell. Determining the level of enrichment of a target chromatin, compared to a non-target chromatin in a cell may be as described in this section below.
A target chromatin of the invention may be isolated using methods known in the art, such as electrophoresis, molecular, immunological and chromatographic techniques, ion exchange, hydrophobic, affinity, and reverse-phase HPLC chromatography, size exclusion chromatography, precipitation, dialysis, chromatofocusing, ultrafiltration and diafiltration techniques, and combinations thereof. For general guidance in suitable purification techniques, see Scopes, R., Protein Purification, Springer-Vertag, NY (1982).
In general, a method of the invention comprises isolating a target chromatin by affinity purification, or affinity purification in combination with other methods of isolating chromatin described above. In a preferred embodiment, a method of the invention comprises isolating a target chromatin by affinity purification. Non limiting examples of affinity purification techniques that may be used to isolate a target chromatin of the invention may include affinity chromatography, immunoaffinity chromatography, size exclusion chromatography, and combinations thereof. See, for example, Roe (ed), Protein Purification Techniques: A Practical Approach, Oxford University Press, 2nd edition, 2001.
In essence, affinity purification of a target chromatin may comprise tagging a target chromatin by contacting the target chromatin of the invention with a tag capable of specifically recognizing and binding one or more portions of a target chromatin. As described in Section (II), a target chromatin from one cell sample, or lysate derived from the cell sample of the invention, but not both of the cell samples, is tagged.
A tag may be capable of specifically recognizing and binding 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 components of a target chromatin. In preferred embodiments, a tag is capable of specifically recognizing and binding one component of a target chromatin.
A tag may be capable of specifically recognizing and binding a component in a target chromatin. A component in a target chromatin may be a nucleic acid sequence in a nucleic acid associated with a target chromatin, a protein associated with a target chromatin, or a chromatin structural or functional feature in a target chromatin. In some embodiments, a tag is capable of specifically recognizing and binding a protein associated with a target chromatin. In other embodiments, a tag is capable of specifically recognizing and binding a chromatin structural or functional feature in a target chromatin. In preferred embodiments, a tag is capable of specifically recognizing and binding a nucleic acid sequence associated with a target chromatin.
A nucleic acid sequence associated with a target chromatin that may be specifically recognized and bound by a tag of the invention may be a nucleic acid sequence normally found in a chromatin of a cell of the invention. In some embodiments, a nucleic acid sequence that may be recognized and bound by a tag is a nucleic acid sequence normally found in a chromatin of a cell of the invention.
Individuals of ordinary skill in the art will recognize that an exogenous chromatin component introduced into a cell to facilitate tagging a target chromatin of the invention cannot and will not disrupt a target chromatin, or a structural or functional feature of a target chromatin. Methods of designing a chromatin component and a tag capable of binding the chromatin component that do not disrupt a chromatin of the invention may depend on the particular application of a method of the invention, and may be determined experimentally. For instance, if an application of a method of the invention comprises promoter function, a tag may be designed to bind anywhere adjacent to the promoter, but without disrupting the promoter.
A tag of the invention may further comprise one or more affinity handles. As used herein, the term “affinity handle” may refer to any handle that may be bound by a substrate for affinity purification, as described below. A tag may comprise one or more than one affinity handle. The inclusion of more than one affinity handle in a tag of the invention may significantly increase the efficiency of affinity purification for a low copy number chromatin target. As such, a tag may further comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more affinity handles. In a preferred embodiment, a tag of the invention comprises one affinity handle.
Affinity handles may include any affinity handle for which a cognate binding agent is readily available. An affinity handle may be an aptamer, an antibody, an antibody fragment, a double-stranded DNA sequence, modified nucleic acids and nucleic acid mimics such as peptide nucleic acids, locked nucleic acids, phosphorodiamidate morpholino oligomers (PMO), a ligand, a ligand fragment, a receptor, a receptor fragment, a polypeptide, a peptide, a coenzyme, a coregulator, an allosteric molecule, non-immunoglobulin scaffolds such as Affibodies, Anticalins, designed Ankyrin repeat proteins and others, an ion, or a small molecule for which a cognate binding agent is readily available. The term “aptamer” refers to a polypeptide or a polynucleotide capable of binding to a target molecule at a specific region. It is generally accepted that an aptamer, which is specific in its binding to any polypeptide, may be synthesized and/or identified by in vitro evolution methods. Non limiting examples of handles that may be suitable for isolating a chromatin may include biotin or a biotin analogue such as desthiobiotin, digoxigenin, dinitrophenol or fluorescein, a macromolecule that binds to a nucleic acid or a nucleic acid binding protein such as the Lac repressor, a zinc finger protein, a transcription activator protein capable of binding a nucleic acid, or a transcription activator-like (TAL) protein, antigenic polypeptides such as protein A, or peptide ‘tags’ such as polyhistidine, FLAG, HA and Myc tags. In preferred embodiments, a tag of the invention comprises an antigenic polypeptide. In other preferred embodiments, a tag of the invention comprises the protein A tagged TAL protein, or derivatives thereof. The TAL protein can be engineered to have binding specificity for a nucleic acid sequence component of a target chromatin of the invention. As such, TAL may be used as an affinity purification tag for purifying a target chromatin. Protein A comprises an affinity handle capable of binding IgG. In exemplary embodiments, a tag of the invention comprises the protein A tagged TAL protein engineered to bind upstream of the GAL1 transcription start site.
In some embodiments, a tag of the invention is a nucleic acid tag capable of binding a nucleic acid sequence component of a chromatin, wherein the nucleic acid sequence component of the chromatin is introduced into a cell of the invention. In some embodiments, a tag of the invention is a nucleic acid tag capable of binding a nucleic acid sequence component of a chromatin, wherein the nucleic acid sequence component of the chromatin is normally present in a cell of the invention. Non-limiting examples of nucleic acid tags capable of binding a nucleic acid sequence component of a chromatin include antisense RNA or DNA nucleic acid tags, and tags comprising modified nucleic acids and nucleic acid mimics such as peptide nucleic acids, locked nucleic acids, phosphorodiamidate morpholino oligomers (PMO). In some embodiments, a tag of the invention is a nucleic acid tag comprising locked nucleotides. For instance, a nucleic acid tag comprising locked nucleotides may be as described in US20110262908 or US20120040857, and a peptide nucleic acid tag may be as described in Boffa et al. 1995 PNAS 92:1901-1905, the disclosures of all of which are incorporated herein in their entirety.
In some preferred embodiments, a tag of the invention is a protein tag capable of binding a nucleic acid sequence component of a chromatin, wherein the nucleic acid sequence component of the chromatin is a nucleic acid sequence normally found in a chromatin of a cell of the invention. Non limiting examples of a protein tag capable of binding a nucleic acid sequence normally found in a chromatin of a cell may be a nucleic acid binding protein such as protein A, the Lac repressor, a zinc finger protein, a transcription activator protein capable of binding a nucleic acid, or a transcription activator-like (TAL) protein. In one embodiment, a tag of the invention is a transcription activator protein capable of binding a nucleic acid sequence normally found in a chromatin of a cell of the invention. In another embodiment, a tag of the invention is a zinc finger protein capable of binding a nucleic acid sequence normally found in a chromatin of a cell of the invention. In an exemplary embodiment, a tag of the invention is a protein A tagged transcription activator-like (TAL) protein capable of binding a nucleic acid sequence normally found in a chromatin of a cell of the invention.
A nucleic acid binding protein tag of the invention may be a wild type nucleic acid binding protein capable of binding a nucleic acid sequence normally found in a target chromatin. Alternatively, a nucleic acid binding protein tag of the invention may be engineered to have binding specificity for a nucleic acid sequence component normally found in a target chromatin of the invention. Individuals of ordinary skill in the art will recognize that nucleic acid binding proteins such as zinc finger proteins, transcription activator proteins, and transcription activator-like (TAL) proteins may be engineered to have novel nucleic acid binding specificity compared to naturally-occurring forms of the proteins. See, for example, U.S. Pat. Nos. 6,453,242 and 6,534,261, and U.S. Pate. Appl. Nos 20110239315, 20120110685, and 20120270273, the disclosures of which are incorporated by reference herein in their entireties. In some embodiments, a nucleic acid binding protein tag of the invention is a wild type nucleic acid binding protein capable of binding a nucleic acid sequence normally found in a target chromatin. In other embodiments, a nucleic acid binding protein tag of the invention is a nucleic acid binding protein engineered to have binding specificity for a nucleic acid sequence component of a target chromatin of the invention. In a preferred embodiment, a nucleic acid binding protein tag of the invention is a zinc finger protein engineered to have binding specificity for a nucleic acid sequence component of a target chromatin of the invention. In an exemplary embodiment, a nucleic acid binding protein tag of the invention is a TAL protein engineered to have binding specificity for a nucleic acid sequence component of a target chromatin of the invention.
In other preferred embodiments, a tag of the invention is a protein tag capable of binding a nucleic acid sequence component of a chromatin, wherein the nucleic acid sequence component of the chromatin is a nucleic acid sequence normally found in a cell of the invention. In exemplary embodiments, a tag of the invention is a protein A tagged TAL protein capable of binding a nucleic acid sequence normally found in a cell of the invention. In an exemplary embodiment, a tag of the invention is a protein A tagged TAL protein capable of binding a nucleic acid sequence normally found in a cell upstream of the transcriptional start site of the GAL1 promoter of a S. cereviseae cell as described in the examples.
A target chromatin may be contacted with a tag at any time during a method of the invention leading to isolation of target chromatin. For instance, a target chromatin may be contacted with a protein tag during cell culture by expressing the protein tag in a cell of the invention. Alternatively, a target chromatin may be contacted with a tag after cell culture but before cell lysis, after cell lysis, or after fragmentation of chromatin to generate chromatin fragments comprising a target chromatin.
In some embodiments, a target chromatin is contacted with a tag after cell culture but before cell lysis. As such, a tag may be introduced into a cell before cell lysis. Methods of introducing a tag into a cell of the invention can and will vary depending on the type of cell, the tag, and the application of a method of the invention. For instance, a nucleic acid tag may be electroporated into a cell after culture. In other embodiments, a target chromatin is contacted with a tag after cell lysis. In yet other embodiments, a target chromatin is contacted with a tag after cell lysis and chromatin fragmentation. In preferred embodiments, a target chromatin is contacted with a tag during cell culture by expressing the tag in a cell of the invention during cell culture. In exemplary embodiments, a target chromatin is contacted with a protein A tagged TAL protein during cell culture by expressing the protein A tagged TAL protein in a cell of the invention during cell culture. In an exemplary embodiment, a target chromatin is contacted with a protein A tagged TAL protein during cell culture by expressing the protein A tagged TAL protein in a yeast cell of the invention during cell culture as described in the examples.
A target chromatin contacted and bound by a tag as described above may be isolated using an affinity handle of the tag. The term “isolated”, may be used herein to describe a purified preparation of a target chromatin that is enriched for the target chromatin, but wherein the target chromatin is not necessarily in a pure form. That is, an isolated target chromatin is not necessarily 100% pure, but may be about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% pure. An isolated target chromatin may be enriched for the target chromatin, relative to a chromatin in the lysed preparation that was not contacted by a tag of the invention. An isolated target chromatin may be enriched by 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 fold relative to a chromatin that is not contacted by a tag of the invention. In some embodiments, an isolated target chromatin is enriched by 2, 3, 4, or 5 fold relative to a chromatin that was not contacted by a tag of the invention. In other embodiments, an isolated target chromatin is enriched by 5, 6, 7, 8, 9, or 10 fold relative to a chromatin that was not contacted by a tag of the invention. In an exemplary embodiment, an isolated target chromatin is enriched 4, 5, or 6 fold relative to a chromatin that was not contacted by a tag of the invention.
A target chromatin contacted and bound by a tag as described above may be isolated using any affinity purification method known in the art. In short, a tagged target chromatin is bound to a substrate capable of binding the affinity handle. The substrate comprising a bound target chromatin may then be washed to remove non-target chromatin and other cell debris, and the target chromatin may be released from substrate. Methods of affinity purification of material comprising an affinity handle are known in the art and may include binding the affinity handle to a substrate capable of binding the affinity handle. The substrate may be a gel matrix such as gel beads, the surface of a container, or a chip. The tagged target chromatin bound to the substrate may then be purified. Methods of purifying tagged molecules are known in the art and will vary depending on the target molecule, the tag, and the substrate. For instance, if the tag is a TAL-protein A tag bound to a site in a target chromatin, the target chromatin may be bound to a magnetic bead substrate comprising IgG, and purified using a magnet.
(e) Protein Extraction, Identification, and Determination of Labeling
Proteins and peptides associated with an isolated target chromatin are extracted from the isolated target chromatin. Methods of extracting proteins from chromatin are generally known in the art of protein biochemistry. Generally, any extraction protocol suitable for isolating proteins and known to those of skill in the art may be used. Extracted proteins may also be further purified before protein identification. For instance, protein extracts may be further purified by differential precipitation, differential solubilization, ultracentrifugation, using chromatographic methods such as size exclusion chromatography, hydrophobic interaction chromatography, ion exchange chromatography, affinity chromatography, metal binding, immunoaffinity chromatography, HPLC, or gel electrophoriesis such as SDS-PAGE and QPNC-PAGE. In a preferred embodiment, extracted proteins are further purified using SDS-PAGE.
Extracted and purified intact proteins and post-translational modification of proteins may then be identified. Alternatively, extracted and purified intact proteins may be further digested, and the resulting peptide fragments are identified. In some embodiments, intact extracted proteins are identified. In preferred embodiments, extracted proteins are further digested, and the resulting peptide fragments are identified. For instance, protein extracts may be fragmented by enzymatically digesting the proteins using a protease such as trypsin. In exemplary embodiments, extracted proteins are further digested as described in the examples.
Methods of identifying proteins or protein fragments are known in the art and may include mass spectrometry (MS) analysis, or a combination of mass spectrometry with a chromatographic technique. Non limiting examples of mass spectrometer techniques may include tandem mass spectrometry (MS/MS), matrix-assisted laser desorption/ionization source with a time-of-flight mass analyzer (MALDI-TOF), inductively coupled plasma-mass spectrometry (ICP-MS), accelerator mass spectrometry (AMS), thermal ionization-mass spectrometry (TIMS), isotope ratio mass spectrometry (IRMS), and spark source mass spectrometry (SSMS). Chromatographic techniques that may be used with MS may include gas chromatography, liquid chromatography, and ion mobility spectrometry. In a preferred embodiment, proteins may be identified using tandem mass spectrometry in combination with liquid chromatography (LC-MS/MS). In another preferred embodiment, post-translational modification of proteins may be identified using tandem mass spectrometry in combination with liquid chromatography (LC-MS/MS).
In the present invention, the method of label-free proteomics is used to categorize whether proteins enriched with a section of chromatin are specific or contaminant. Label-free methods of quantifying proteins or protein fragments are known in the art. In label-free quantitative proteomics, each sample is separately prepared, then subjected to individual methods of identifying proteins or protein fragments which may include LC-MS/MS or LC/LC-MS/MS. According to the invention, one sample comprises a target chromatin that is tagged in the cell sample and one sample comprises a target chromatin that is untagged in the cell sample. Label-free protein quantification is generally based on two categories of measurement. In the first are the measurements of ion intensity changes such as peptide peak areas or peak heights in chromatography. The second is based on the spectral counting of identified proteins after MS/MS analysis. Peptide peak intensity or spectral count is measured for individual LC-MS/MS or LC/LC-MS/MS runs and changes in protein abundance are calculated via a direct comparison between different analyses. In a preferred embodiment, the proteins identified using mass spectrometry are quantified and identified as enriched in the sample containing the tagged target chromatin compared to the sample containing the untagged target chromatin using label-free proteomics. In an exemplary embodiment, the proteins identified using mass spectrometry are quantified and identified as enriched in the sample containing the tagged target chromatin compared to the sample containing the untagged target chromatin using spectral counting.
The method of protein quantification by spectral count is known in the art and is reviewed in Zhu et al., J Biomed Biotechnol 2010, which is incorporated by reference herein. In spectral counting, relative protein quantification is achieved by comparing the number of identified MS/MS spectra from a protein of one sample to the same protein in the other sample. In the present invention, one sample comprises a target chromatin that is tagged and another sample comprises a target chromatin that is untagged. Protein quantification in spectral counting utilizes the fact that an increase in protein abundance typically results in an increase in the number of its proteolytic peptides, and vice versa. This increased number of (tryptic) digests then usually results in an increase in protein sequence coverage, the number of identified unique peptides, and the number of identified total MS/MS spectra (spectral count) for each protein.
As such, determining the abundance of an identified protein in a tagged chromatin sample compared to the same protein in an untagged chromatin sample, may determine if the protein was specifically associated with a target chromatin of the invention. If an identified protein associated with a target chromatin is in enriched in a tagged chromatin sample compared to the same protein in an untagged chromatin sample, then the protein was specifically associated with a target chromatin of the invention. If an identified protein is not enriched in a tagged chromatin sample compared to an untagged chromatin sample, then the protein is non-specifically associated with a target chromatin of the invention.
A skilled artisan in spectral counting will appreciate that normalization and statistical analysis of spectral counting datasets are necessary for accurate and reliable detection of protein changes. Since large proteins tend to contribute more peptide/spectra than small ones, a normalized spectral abundance factor (NSAF) is defined to account for the effect of protein length on spectral count. NSAF is calculated as the number of spectral counts (SpC) identifying a protein, divided by the protein's length (L), divided by the sum of SpC/L for all proteins in the experiment. NSAF allows the comparison of abundance of individual proteins in multiple independent samples and has been applied to quantify the expression changes in various complexes.
In the present invention, to measure enrichment of a protein, the normalized spectral abundance factor (NSAF) is calculated for each protein in each lane of an SDS-PAGE gel by dividing the number of spectral counts (normalized for the size of the protein) of a given protein by the sum of all normalized spectral counts of all proteins in the gel lane. The enrichment level for each protein is identified by calculating the fold enrichment (tagged chromatin/untagged chromatin) using the NSAF values. In an exemplary embodiment, proteins enriched in a sample containing a tagged target chromatin compared to a sample containing an untagged target chromatin are enriched by at least about 2 fold. In other embodiments, proteins enriched in a sample containing a tagged target chromatin compared to a sample containing the untagged target chromatin are enriched by at least about 1.5 fold. In other embodiments, proteins enriched in a sample containing a tagged target chromatin compared to a sample containing an untagged target chromatin are enriched by at least about 3 fold, about 4 fold, about 5 fold, about 6 fold, about 7 fold, about 8 fold, about 9 fold, about 10 fold, about 11 fold, about 12 fold, about 13 fold, about 14 fold, about 15 fold, about 16 fold, about 17 fold, about 18 fold, about 19 fold or about 20 fold. As such, a protein enriched by at least about 2 fold in a tagged chromatin sample compared to an untagged chromatin sample, is specifically associated with the chromatin. For instance, a baseline for non-specifically associated proteins may be proteins enriched by less than about 1.5 fold in a tagged chromatin sample compared to an untagged chromatin sample, wherein one or more proteins are not associated with chromatin. Non-limiting examples of proteins not associated with a chromatin may include enzymes required for metabolism, receptors, and ribosomal proteins. In preferred embodiments, proteins not associated with a chromatin are ribosomal proteins, and a baseline for non-specifically associated proteins is an enrichment less than about 1.5 fold in a tagged chromatin sampled compared to an untagged chromatin sample. In an exemplary embodiment, proteins or protein fragments enriched by at least 15 fold in a tagged chromatin sample compared to an untagged chromatin sample are specifically associated with a target chromatin.
In preferred embodiments, a target chromatin is tagged in one cell sample and a target chromatin is untagged in a second cell sample, and MS analysis is used to identify proteins or protein fragments isolated during affinity purification of each sample, and label-free proteomics is used to determine if a protein or a protein fragment is specifically or non-specifically associated with the target chromatin. Methods of deriving MS data to identify proteins or protein fragments are known in the art, and may include using known computational techniques to distill MS data such as Mascot Distiller, Rosetta Elucidator, and MaxQuant. In some embodiments, MS data is derived using Rosetta Elucidator. In other embodiments, MS data is derived using MaxQuant. In preferred embodiments, MS data is derived using Mascot Distiller.
(f) Applications
Applications of the invention may be as described in Section I(f) above.
III. Kits
In other aspects, the present invention provides kits for isolating and identifying proteins specifically associated with a chromatin. The kits may comprise, for example, a growth medium comprising a metabolic label, or a metabolic label that may be added to a growth medium, and cells comprising a tagged target chromatin, and instructions describing a method of the invention. A kit may further comprise material necessary for affinity purification of a tagged target chromatin, and a sample comprising metabolically labeled and unlabeled non-specifically associated proteins for determination of a baseline for non-specifically associated proteins. A kit my also comprise material necessary for affinity purification of a tagged target chromatin, and instructions describing a method of the invention.
Cells, and methods of the invention may be as described in Section I and Section II above.
EXAMPLES
The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent techniques discovered by the inventors to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.
Introduction for Examples 1-3
It has long been appreciated that chromatin-associated proteins and epigenetic factors play central roles in cell-fate reprogramming of genotypically identical stem cells through lineage-specific transcription or repression of precise genes and large chromosomal regions (Martin, 1981; Ho and Crabtree, 2010; Rossant, 2008). However, the hierarchy of chromatin-templated events orchestrating the formation and inheritance of different epigenetic states remains poorly understood at a molecular level. Since misregulation of chromatin structure and post-translational modification of histones (PTMs) is linked to cancer and other epigenetic diseases (Jones and Baylin, 2007; Chi et al., 2010), it is imperative to establish new methodologies that will allow comprehensive studies and unbiased screens for participants in epigenetic mechanisms. Unfortunately, defining how chromatin regulators collectively assemble and operate on a precise region of the genome is difficult to elucidate; there are no current methodologies that allow for determination of all proteins present at a defined, small region of chromatin.
Technical challenges have precluded the ability to determine positioning of chromatin factors along the chromosome. Chromatin immunoprecipitation (ChIP) assays have been used to better understand genome-wide distribution of proteins and histone modifications within a genome at the nucleosome level (Dedon at al., 1991; Ren et al., 2000; Pokholok et al., 2005; Robertson et al., 2007; Johnson et al., 2007; Barski at al., 2007; Mikkelsen et al., 2007). However, major drawbacks of ChIP-based chromatin enrichment methods include experiments that are largely confined to examining singular histone PTMs or proteins rather than simultaneous profiling of multiple targets, the inability to determine the co-occupancy of particular histone PTMs, and that ChIP is reliant on the previous identification of the molecular target. Affinity purification approaches have been devised for the isolation of a chromatin region (Griesenbeck et al., 2003; Agelopoulos et al., 2012); however, these approaches were not done at a level for proteomic analysis and they do not provide a mechanism for determining the specificity of protein interactions. More recently, groups biochemically enriching for intact chromatin have reported characterization of proteins associated with large chromatin structures such as telomeres (Dejardin and Kingston, 2009) and engineered plasmids (Akiyoshi et al., 2009; Unnikrishnan et al., 2010); however, these approaches do not enrich for a small integrated genomic locus and do not employ specialized mass spectrometric techniques to detect protein contamination in purified material.
We sought to compare differences in chromatin between the transcriptionally active and silent states of a single genomic locus, and developed a technology, called chromatin affinity purification with mass spectrometry (ChAP-MS). ChAP-MS provides for the site-specific enrichment of a given  ̃1,000 base pair section of a chromosome followed by unambiguous identification of both proteins and histone PTMs associated with this chromosome section using highly selective mass spectrometry. Using ChAP-MS, we were able to purify chromatin at the Saccharomyces cerevisiae GAL.1 locus in transcriptionally silent and active states. We identified proteins and combinatorial histone PTMs unique to each of these functional states and validated these findings with ChIP. The ChAP-MS technique will greatly improve the field of epigenomics as an unbiased approach to study regulatory mechanisms on chromatin.
Example 1
ChAP-MS Technology
FIG. 1A provides an overview of the ChAP-MS approach that was used to screen for proteins and histone PTMs associated with a specific genomic locus in transcriptionally active or repressive states. A LexA DNA binding site was engineered immediately upstream of the GAL1 start codon in a S. cerevisiae strain constitutively expressing a LexA-Protein A (LexA-PrA) fusion protein. The LexA DNA binding site directs the localization of the LexA-PrA protein affinity “handle” to the GAL1 promoter in vivo. The positioning of the LexA DNA was designed to specifically enrich for chromatin-associated proteins and histone PTMs regulating gene expression near the transcriptional start site of GAL1. This strain was cultured in glucose to repress gene transcription, or galactose to activate gene transcription. Following in vivo chemical crosslinking to preserve the native protein-protein interactions at GAL1 promoter chromatin, the chromatin was sheared to  ̃1,000 base pair sections. The PrA moiety of the LexA-PrA fusion protein was then used to affinity purify the  ̃1,000 base pair section of chromatin at the 5′ end of the GAL1 gene for high resolution mass spectrometric identification of proteins and histone PTMs. It was anticipated that culturing these cells in glucose would result in the isolation of proteins and PTMs correlated to silent chromatin, while culturing cells in the presence of galactose would purify histone PTMs and proteins, like RNA polymerase, that are involved with active gene transcription.
The GAL1 gene is present at one copy per haploid cell; due to the relative low abundance of the targeted chromatin region in cellular lysates, it was fully anticipated that proteins nonspecifically associating with GAL1 chromatin would complicate analysis of the resulting purified material. Copurification of nonspecifically associating proteins is one of the major complications of affinity purifications; however, isotopic labeling of media provides a means to gauge in vivo protein-protein interactions and quantitate differences in peptide abundance (Smart et al., 2009; Tackett et al., 2005a). The inventors had previously developed a variation of this labeling technique called iDIRT (isotopic differentiation of interactions as random or targeted) that provides a solution for determining which coenriched proteins are specifically or nonspecifically associated with a complex of proteins (Smart et al., 2009; Tackett et al., 2005a). The iDIRT technique was adapted (as described in FIG. 1B) to control for proteins nonspecifically enriching with LexA-PrA and the resin. By using this adaptation of iDIRT on chromatin enriched from active and repressed chromatin states, the proteins nonspecifically enriching with the isolated GAL1 chromatin section were identified. The strain containing the LexA DNA binding site and LexA-PrA fusion protein was cultured in isotopically light media, while a strain lacking the LexA DNA binding site (but still containing the LexA-PrA fusion protein) was cultured in isotopically heavy media (13C615N2-lysine). N lysine). Following isolation of the cells, the light and heavy strains were mixed and colysed. The growth and mixing of light/heavy strains was performed separately under glucose and galactose growth conditions. The affinity purification of the GAL1 chromatin was performed from this mixture of light/heavy lysates. Proteins and histone PTMs specifically associated with the GAL1 chromatin containing the LexA DNA binding site were isotopically light as they arose from the cells grown in light media. Proteins that were nonspecific to the purification were a 1:1 mix of light and heavy as they were derived equally from the light and heavy lysates. Analysis of peptides from the enriched proteins with high-resolution mass spectrometry was used to determine the level of isotopically light and heavy proteins, thereby determining whether the detected protein was either a specific in vivo constituent of GAL1 chromatin or a nonspecific contaminant.
Example 2
Affinity Purification of a Specific Chromosome Section
To provide for enrichment of a specific chromosome section, a DNA affinity handle was engineered at the GAL1 gene in S. cerevisiae (FIG. 2A). A LexA DNA binding site was inserted via homologous recombination just upstream of the GAL1 start codon to create strain LEXA::GAL1. To create this strain, GAL1 was genomically deleted with URA3 in the W303a background, and then the GAL1 gene was reinserted with the upstream LEXA DNA sequence by homologous recombination. A plasmid constitutively expressing LexA-PrA was introduced into the strain to create LEXA::GAL1 pLexA-PrA (FIG. 2A). This strain provides a DNA affinity handle at the GAL1 gene and a protein affinity handle for specific enrichment. To determine if insertion of this LexA DNA binding site at GAL1 affected gene transcription, LEXA::GAL1 pLexA-PrA was cultured in glucose to repress gene transcription at GAL1, and separately in galactose to activate transcription. From these growths, cDNA was prepared and real-time PCR was used to measure the activation of GAL1 transcription in the presence of galactose (FIG. 2B). Insertion of the LexA DNA binding site just upstream of the GAL1 start codon did not drastically affect the activation of gene transcription; thus, this strain was used for ChAP-MS purification of GAL1 chromatin in the transcriptionally active and silent states.
To determine the effectiveness of isolation of GAL1 chromatin, the stringency and specificity of different purification conditions was analyzed. Purification of protein complexes under increasing stringencies such as high salt levels provides for the isolation of fewer nonspecifically interacting proteins (Smart et al., 2009; Taverna et al., 2006). Since the proteins purified with GAL1 chromatin will be chemically crosslinked, the stringency of the purification can potentially be quite high. Indeed, ChIP-qPCR against GAL1 showed that the PrA-based purification can survive relatively stringent conditions (FIG. 3A). From these studies, 1M NaCl and 1M urea were selected for future purifications, as these conditions are quite stringent and provide for enrichment of the GAL1 chromatin. Using an identical ChIP approach, the specificity of the GAL1 chromatin enrichment was determined (FIG. 3B). Using primers targeted to the indicated regions of chromatin surrounding GAL1, it was detected that the first 1,000 base pair section of the GAL/gene was indeed enriched. Enrichment of GAL1 chromatin was observed at a similar level under glucose and galactose growth conditions (FIG. 3C). The slightly less efficient isolation under galactose growth conditions may reflect availability of the DNA affinity site due to alterations in chromatin structure.
Example 3
ChAP-MS Analysis of Transcriptionally Active Anti Silent GAL1 Chromatin
Strain LEXA::GAL1 pLexA-PrA was subjected to the ChAP-MS procedure as outlined in FIG. 1. Strain LEXA::GAL1 pLexA-PrA was grown in isotopically light media, while strain pLexA-PrA was grown in isotopically heavy media. Following growth of each strain to mid-log phase, the cells were treated with 1.25% formaldehyde to trap protein interactions on the chromosomes. A detailed analysis of the amount of formaldehyde crosslinking required to preserve the in vivo state of chromatin during affinity purifications was recently published by the inventors (Byrum et al., 2011a, 2011b). Approximately 2.5×1011 LEXA::GAL1 pLexA-PrA cells were mixed with an equivalent amount of isotopically heavy pLexA-PrA cells (separately for media containing glucose and galactose) and then subjected to lysis under cryogenic conditions with a Retch MM301 ball mill (Tackett et al., 2005a). Lysates were suspended in 20 mM HEPES (pH 7.4), 0.1% Tween 20, 1 M NaCl, 1 M urea, and 2 mM MgCl2. Lysates were then subjected to sonication and chromatin was sheared to sections of  ̃1,000 base pairs. LexA-PrA was collected on IgG-coated Dynabeads and coenriching proteins were resolved by SDS-PAGE and visualized by Coomassie staining (FIG. 4A). Gel lanes were sliced into 2 mm sections and subjected to in-gel trypsin digestion (Smart et al., 2009; Tackett et al., 2005a, 2005b). Peptides from proteins were identified by high-resolution mass spectrometry with a Thermo Velos Orbitrap mass spectrometer equipped with a Waters nanoACQUITY UPLC system. Proteins and PTM-containing peptides were identified and the level of isotopically light to heavy peptide was calculated with Mascot Distiller (Smart et al., 2009), Representative spectra are shown in FIG. 4B-D. Major bands observed in the gel lanes correspond to the affinity purification protein LexA-PrA and IgG chains as anticipated. Other proteins identified correspond to specifically and nonspecifically enriched proteins. Tables 1 and 2 list the proteins identified and percent isotopically light peptides (352 proteins from the glucose ChAP-MS and 399 proteins from the galactose ChAP-MS).
Once proteins were identified, a baseline was established for nonspecifically associated proteins in accordance to the iDIRT approach (Smart et al., 2009). Nonspecifically enriching ribosomal proteins were used to establish the nonspecifically associating baseline (Smart et al., 2009). The average percent isotopically light peptides from 20 ribosomal proteins from the glucose and galactose growth conditions were used to establish this nonspecifically associating baseline (Table 3). This resulted in a nonspecifically associating baseline of 49.93%±2.12% light for the glucose ChAP-MS and 66.8%±7.1% light for the galactose ChAP-MS (FIG. 5). Proteins were categorized as specifically associating with GAL1 chromatin if the percent light was greater than 2 SDs above the ribosomal level (Smart et al., 2009). FIG. 5 shows the proteins and histone PTMs specifically enriched with GAL1 chromatin under glucose and galactose growth conditions. Tables 4 and 5 list proteins that were identified as specifically enriched in both the glucose and galactose ChAP-MS analyses. Specifically enriched proteins or histone PTMs known to be involved in transcriptional regulation are listed in FIG. 5. For the glucose and galactose ChAP-MS analyses, 11 and 17 (respectively) additional proteins were detected as specifically enriched (FIG. 5, Tables 4 and 5). These additional proteins are abundant metabolic and heat shock proteins that are typical contaminants and false positives for this study. However, narrowing down 352 proteins identified from the glucose ChAP-MS and 399 proteins from the galactose ChAP-MS to 12 proteins and 27 proteins/PTMs specifically enriched produced a short list of candidates that was easily validated.
The ChAP-MS analyses of GAL1 chromatin revealed association of Gal3, Spt16, Rpb1, Rpb2, H3K14ac, H3K9acK14ac, H3K18acK23ac, H4K5acK8ac, and H4K12acK16ac under transcriptionally active conditions, while transcriptionally repressive conditions showed the enrichment of H3K36me3. In order to validate the ChAP-MS approach, standard ChIP was performed to specific interactions detected in the transcriptionally active and silent chromatin state at GAL1 (FIG. 6). These ChIP experiments validated the proteins and PTMs found associated with the transcriptionally active and repressed states of GAL1 chromatin determined from the ChAP-MS approach.
Discussion for Examples 1-3
The chromatin biology and epigenomics research communities have been limited to biased technologies that restrict targeted genome localization studies to previously identified proteins or histone PTMs. Here, a newly developed technology, called ChAP-MS, is described that circumvents this limitation by providing for isolation of a  ̃1,000 base pair section of a chromosome for proteomic identification of specifically bound proteins and PTMs. In essence, the ChAP-MS approach allows one to take a “molecular snapshot” of chromatin dynamics at a specific genomic locus. Furthermore, employing this approach to target other chromatin regions will likely provide unprecedented insight on a variety of epigenetic regulatory mechanisms, chromatin structure, and genome metabolism.
Validation of the ChAP-MS Approach
The ChAP-MS approach was validated on the well-studied GAL1 locus in S. cerevisiae. The GAL1 gene is activated for gene transcription in the presence of galactose, while glucose represses transcription. Accordingly, it was rationalized that a purified  ̃1,000 base pair section of chromatin at the 5′ end of the GAL1 gene from cells grown in galactose would contain histone PTMs correlated with active transcription and cellular machinery necessary for transcription, while the same chromatin section from cells grown in glucose would be enriched with histone PTMs associated with transcriptional repression. Prior publications have documented that H3 acetylation is enriched on the 5′ end of the active galactose-induced GAL1 gene, while in the presence of glucose it contains H3K36me3 (Shukla et al., 2006; Houseley et al., 2008). Results presented in the Examples herein with ChAP-MS, support each of these prior findings (FIG. 5). Furthermore, the presence of doubly acetylated histones (H3K9acK14ac, H3K18acK23ac, H4K5acK8ac, H4K12acK16ac) during transcriptional activation was identified. This demonstrates how ChAP-MS may be used to study the combinatorial “code” of histone modifications at given chromosome regions without the need for prior identification of PTMs, PTM-specific antibodies, or sequential chromatin put-downs. Considering H4K12acK16ac for example, the identification of the double acetylation is unique to the ChAP-MS approach as antibodies to this double acetylation do not exist, thus one could not have performed a biased ChIP analysis. Additionally, it has been reported that commercially available antibodies to single acetylation at H4K12 or H4K16 are cross-reactive with other H4 acetylations and that double acetylation of H4K12K16 significantly alters the specificity of the antibody to the singly acetylated sites (Bock et al., 2011) —a limitation specific to antibodies used in biased ChIP studies and not to the unbiased ChAP-MS approach that uses quantitative mass spectrometric readout. The ChAP-MS approach simultaneously identified the presence of RNA polymerase (Rpb1, Rpb2) and FACT component Spt16 (which aids in reorganizing chromatin for RNA pol activity) under these transcriptionally active conditions. Also of interest was the identification of Gal3 at actively transcribing GAL1, which has previously been shown to inhibit the repressive activity of Gal80 at the GAL10/GAL1 locus (Platt and Reece, 1998). It was demonstrated how the ChAP-MS approach may be utilized to study chromatin dynamics at GAL1 under different states of gene transcription. Of particular interest for future functional studies may be the upstream activating sequence which binds the Gal4 actuator and Gal80 repressor which may allow better understand of the events surrounding the switch from repression to activation at GAL1 and GAL10, as well as the middle and 3′ end of GAL1 to understand the processes of elongation and termination, respectively.
Utility of ChAP-IVIS as a General Tool for Studying Chromatin Biology
The ChAP-MS technology presented here demonstrates the ability to purify a unique chromosome section on the order of four to five nucleosomes in length from an in vivo source that can subsequently be subjected to sensitive proteomic studies. ChAP-MS has numerous advantages relative to traditional ChIP, including the ability to unbiasedly detect proteins/PTMs at a specific genomic locus and the identification of combinatorial histone modifications on a single histone molecule. Furthermore, ChAP-MS only requires approximately an order of magnitude more cells relative to biased ChIP studies, which is a huge advantage if doing more than ten blind ChIP studies at a given region is factored in (chances are many antibodies for many proteins would be heavily invested in, trying to guess a specifically bound protein/PTM). In this regard, ChAP-MS is a more cost-effective option for characterizing specifically bound proteins and histone PTMs relative to ChIP. Future derivations of this technology may employ targeted mass spectrometric approaches for better determination of combinatorial histone PTMs as well as identification of other regulatory PTMs on nonhistone proteins from these isolated sections (Taverna et al., 2007). Given the sensitivity of the mass spectrometry analysis employed and the relatively modest biological starting material, the findings presented in the Examples herein also establish a framework for applying ChAP-MS to profile across entire regions of chromosomes or investigate higher eukaryotic systems. Regardless, any advances that permit ChAP-MS analysis of in vivo untagged or unaltered samples, like tissues, will undoubtedly have valuable applications for investigating altered gene transcription mechanisms in human disease states, as this technique could provide a comprehensive way to intelligently identify targets for therapeutics.
Experimental Procedures for Examples 1-3
Construction of the LEXA::GAL 1 pLexA-PrA Strain
The LEXA::GAL1 pLexA-PrA strain used to affinity enrich GAL1 chromatin was designed to have a LexA DNA binding site just upstream of the GAL1 start codon and contains a plasmid constitutively expressing a LexA-PrA fusion protein. In S. cerevisiae from the W303a background, the GAL1 gene was genomically replaced with URA3 using homologous recombination. Next, the GAL1 gene (+50 base pairs up- and downstream) was PCR amplified with primers that incorporated a LexA DNA binding site (5′-CACTTGATACTGTATGAGCATACAGTATAATTGC) immediately upstream of the GAL1 start codon. This LEXA::GAL1 cassette was transformed into the gal1::URA3 strain and selected for growth with 5-fluoroorotic acid, which is lethal in URA3 expressing cells. Positive transformants were sequenced to ensure homologous recombination of the cassette to create the LEXA::GAL1 strain. A plasmid that constitutively expresses LexA-PrA fusion protein with TRP selection was created by amplification of the PrA sequence from template pOM60 via PCR and subcloning into the Sac1/Sma1 ends of the expression plasmid pLexA-C. Transforming this plasmid into the LEXA:GAL1 strain gave rise to the LEXA:GAL1 pLexA-PrA strain. Additionally, a control used in these studies was W303a S. cerevisiae transformed only with pLexA-PrA.
Cell Culture
Strains LEXA:GAL1 pLexA-PrA and pLexA-PrA were grown in yeast synthetic media lacking tryptophan to mid-log phase at 30° C. LEXA:GAL1 pLexA-PrA strain growths were done with isotopically light lysine, while strain pLexA-PrA was cultured exclusively with isotopically heavy 13C615N2-lysine. For each strain, 12 l of media containing either 2% glucose or 3% galactose were grown to yield  ̃5×1011 cells per growth condition. At mid-log phase, the cultures were crosslinked with 1.25% formaldehyde for 5 min at room temperature and then quenched with 125 mM glycine for 5 min at room temperature. Cells were harvested by centrifugation (2,500×g) and frozen in liquid nitrogen as pellets in suspension with 20 mM HEPES (pH 7.4), 1.2% polyvinylpyrrolidone (1 ml/10 g of cell pellet). Frozen cell pellets were mixed as follows at 1:1 cell weight ratios: (1) LEXA:GAL1 pLexA-PrA isotopically light in glucose plus pLexA-PrA isotopically heavy control in glucose (2) LEXA:GAL1 pLexA-PrA isotopically light in galactose plus pLexA-PrA isotopically heavy control in galactose. Cell mixtures were cryogenically lysed under liquid nitrogen temperature with a Retsch MM301 ball mill (Smart et al., 2009; Tackett et al., 2005a).
ChAP-MS Procedure
Each of the following two cell lysates were processed for purification of GAL1 chromatin: (1) LEXA:GAL1 pLexA-PrA isotopically light in glucose plus pLexA-PrA isotopically heavy control in glucose, referred to as the glucose ChAP-MS, and (2) LEXA:GAL1 pLexA-PrA isotopically light in galactose plus pLexA-PrA isotopically heavy control in galactose, referred to as the galactose ChAP-MS. Twenty grams of frozen cell lysate ( ̃5×1011 cells) was used for each of the glucose and galactose ChAP-MS analyses. ChAP-MS steps were performed at 4° C. unless otherwise noted. Lysates were resuspended in 20 mM HEPES (pH 7.4), 1 M NaCl, 2 mM MgCl2, 1 M urea, 0.1% Tween 20, and 1% Sigma fungal protease inhibitor cocktail with 5 ml buffer per gram of frozen lysate. Lysates were subjected to sonication with a Diagenode Bioruptor UCD-200 (low setting, 30 s on/off cycle, 12 min total time) in 20 ml aliquots to yield  ̃1 kb chromatin fragments. Supernatants from sonicated lysates were collected by centrifugation at 2,000×g for 10 min. Dynabeads (80 mg) coated with rabbit IgG were added to the lysates and incubated for 4 hr with constant agitation (Byrum et al., 2012a). Dynabeads were collected with a magnet and washed 5 times with the purification buffer listed above and 3 times with 20 mM HEPES (pH 7.4), 2 mM MgCl2, 10 mM NaCl, 0.1% Tween 20. Washed Dynabeads were treated with 0.5 N ammonium hydroxide/0.5 mM EDTA for 5 min at room temperature to elute proteins. Eluants were lyophilized with a Savant SpeedVac Concentrator. Lyophilized proteins were resuspended in Laemmli SDS-PAGE loading buffer, heated to 95° C. for 20 min, resolved with 4%-20% tris-glycine Invitrogen precast gels, and visualized by colloidal Coomassie staining.
High-Resolution Mass Spectrometry and Data Analysis
Gel lanes were sliced into 2 mm sections and subjected to in-gel trypsin digestion (Byrum et al., 2011a, Byrum et al., 2011b, Byrum et al., 2012a; Tackett et al., 2005b). Peptides were analyzed with a Thermo Velos Orbitrap mass spectrometer coupled to a Waters nanoACQUITY liquid chromatography system (Byrum et al., 2011b). Using a data-dependent mode, the most abundant 15 peaks were selected for MS2 from a high-resolution MS scan. Proteins were identified and the ratio of isotopically light/heavy lysine-containing tryptic peptide intensity was determined with Mascot and Mascot Distiller. The search parameters included: precursor ion tolerance 10 ppm, fragment ion tolerance 0.65 Da, fixed modification of carbamidomethyl on cysteine, variable modification of oxidation on methionine, and two missed cleavages possible with trypsin. A threshold of 95% confidence for protein identification, 50% confidence for peptide identification and at least two identified peptides per protein was used, which gave a 2% peptide false discovery rate. All specifically associating protein identifications and ratios were manually validated.
A baseline was established for nonspecifically associated proteins with nonspecifically enriched ribosomal proteins (Smart et al., 2009). The average percent isotopically light peptides from 20 ribosomal proteins from the glucose and galactose growth condition were used to establish this nonspecifically associated baseline. This resulted in a nonspecifically associated baseline of 49.93%±2.12% light for the glucose ChAP-MS and 66.8%±7.1% light for the galactose CHAP-MS. Proteins were categorized as specifically associating if the percent light was greater than 2 SDs above the ribosomal level (Tables 4 and 5) (Smart et al., 2009). Duplicate ChAP-MS procedures showed Pearson and Spearman correlation coefficient p values of <0.001.
ChIP and Gene Transcription Assays
ChIP and gene transcription assays were performed as previously reported (Tackett et al., 2005b; Taverna et al., 2006). Assays were performed in triplicate and analyzed by real time PCR.
Introduction for Examples 4-5
One of the most compositionally diverse structures in a eukaryotic cell is a chromosome. A multitude of macromolecular protein interactions and epigenetic modifications must properly occur on chromatin to drive functional aspects of chromosome biology like gene transcription, DNA replication, recombination, repair and sister chromatid segregation. Analyzing how proteins interact in vivo with chromatin to direct these activities and how epigenetics factors into these mechanisms remains a significant challenge owing to the lack of technologies to comprehensively analyze protein associations and epigenetics at specific native chromosome sites. Chromatin immunoprecipitation (ChIP) assays have traditionally been used to better understand genome-wide distributions of chromatin-associated proteins and histone post-translational modifications (PTMs) at the nucleosome level (Cermak et al., 2011). However, major drawbacks of current ChIP-based methods include their confinement to examining singular histone PTMs or proteins rather than simultaneous profiling of multiple targets, the inability of ChIP to directly determine the co-occupancy of particular histone PTMs and that ChIP is reliant on the previous identification and development of affinity reagents against the molecular target. A more comprehensive and unbiased approach would be the biochemical isolation of a specific native genomic locus for proteomic identification of proteins-associated and histone PTMs. Similar approaches have been performed for large structures like telomeres, engineered plasmids or engineered loci (Griesenbeck et al., 2003; Dejardin and Kingston, 2009; Hoshino and Fuji, 2009; Akiyoshi et al., 2009; Unnikrishnan et al., 2010; Byrum et al., 2012b); however, the proteomic analysis of a small native genomic region without genomic engineering has yet to be performed. To work toward proteomic studies of native chromatin regions (i.e. sections of chromatin that are unaltered genetically and spatially the genome), we recently developed a technique termed Chromatin Affinity Purification with Mass Spectrometry (ChAP-MS) that provides for the enrichment of a native 1-kb section of a chromosome for site-specific identification of protein interactions and associated histone PTMs (Byrum et al., 2012b). This ChAP-MS approach uses the association of an ectopically expressed affinity-tagged LexA protein with a genomically incorporated LexA DNA binding site for site-specific chromatin enrichment. The ChAP-MS approach provides for the isolation of chromatin from the native site in the chromosome; however, one must genomically engineer a LexA DNA binding site, which could alter the native state of the chromatin and which requires a biological system readily amendable to genomic engineering.
To alleviate genomic engineering for affinity enrichment of chromatin sections, we report the use of modified transcription activator-like (TAL) effector proteins to site-specifically target a native section of a chromosome for purification and proteomic analysis. We term this approach TAL-ChAP-MS (FIG. 7A). TAL effector proteins are from Xanthomonas, which infects plants and translocates TAL effectors into cells where they serve as transcription activators (Scholze and Boch, 2010; Scholze and Boch, 2011; Doyle et al., 2012). TALs contain a central domain of 18 tandem repeats of 34 amino acids each, which direct sequence-specific DNA binding (Doyle et al., 2012; Cermak et al., 2011). Binding to a given nucleobase in DNA is determined by two adjacent amino acids (12 and 13) within each of the 18 repeats (Scholze and Boch, 2010). Thus, by mutating these amino acids in each of the 18 tandem repeats, one can ‘program’ binding to a given 18-nt region of DNA in vivo. TAL proteins have been validated in cell culture for targeting nucleases for genome editing and for targeting transcription activators (Miller et al., 2011; Geissler et al., 2011). To test the ability of a TAL protein to serve as an affinity enrichment reagent for native chromatin isolation, a TAL protein was designed that bound a unique 18-nt region of DNA in the promoter region of the GAL1 gene in Saccharomyces cerevisiae (FIG. 7B). We chose to analyze proteins and histone PTMs regulating the galactose-induced gene transcription of GAL1 because (1) this is a well-studied genomic locus, which will provide for proof-of-principle analysis, and (2) we previously used this locus to develop the ChAP-MS technique (Byrum et al., 2012b); thus, a comparison can be made to the new TAL-ChAP-MS approach.
One of the major complications for studying specific protein associations with purified protein complexes or with chromatin is the co-enrichment of non-specifically associating proteins. This particularly becomes an issue when studying low copy number entities such as a single genomic locus. With the advancement of high-resolution and sensitive mass spectrometry in recent years, it has been suggested that >109 cell equivalents are needed to study single genomic loci with proteomic approaches (Chait, 2011). In agreement, our ChAP-MS studies used 1011 cells for isolation of GAL1 promoter chromatin at levels sufficient for proteomic analysis (Byrum et al., 2012b). When scaling up purifications of low copy entities to meet the sensitivity necessary for high-resolution mass spectrometric analysis, the issue of co-purifying abundant non-specific proteins becomes a major challenge. In the ChAP-MS approach (Byrum et al., 2012b), we used an isotope-labeling strategy to categorize whether a protein co-enriching with a section of chromatin was specifically associated or a contaminant. Limitations for isotope-labeling approaches are cost and having biological systems of study that are amendable to stable isotope-labeling with amino acids. To circumvent the use of isotope-labeling, we now have incorporated label-free quantitative mass spectrometry in the TAL-ChAP-MS workflow. The described TAL-ChAP-MS approach can therefore provide for the purification of a native chromatin region for label-free quantitative proteomic analysis, which will greatly simplify studies of how proteins and combinatorial histone PTMs regulate chromosome metabolism.
Example 4
Development of TAL-ChAP-MS
A schematic of the TAL-ChAP-MS approach to purify native chromatin for proteomic analysis is shown in FIG. 7A. To demonstrate the utility of the TAL-ChAP-MS approach, we used a TAL protein to target the promoter chromatin region upstream of the galactose-inducible GAL1 gene in S. cerevisiae (FIG. 7B). Yeast cells were grown in the presence of galactose to induce transcription of the GAL1 gene, which will recruit proteins and histone PTMs that activate transcription. A wild-type culture and a culture of cells containing a plasmid that expressed a PrA-tagged TAL protein that bound the GAL1 promoter region were grown and subjected to in vivo formaldehyde cross-linking to preserve chromatin structure during purification (Byrum et al., 2011a; Byrum et al., 2011b). Following cryogenic cell lysis and sonication of chromatin sections to  ̃1 kb, each lysate was independently subjected to affinity enrichment of PrA with IgG-coated Dynabeads. Proteins co-enriching with TAL-PrA from the cells containing the pTAL-PrA plasmid and those enriching as contamination from the control cells with no plasmid were identified by high-resolution mass spectrometry. Using label-free quantitative analyses, the relative enrichment of proteins and histone PTMs specifically hound to the GAL1 promoter chromatin were identified.
Saccharomyces cerevisiae cells were transformed with pTAL-PrA, and protein expression was validated by western blotting (FIG. 7C). To evaluate whether TAL-PrA expression affected galactose-induced transcription of GAL 1, cDNA was prepared from wild-type and wild-type (+pTAL-PrA) cells under glucose (transcriptionally repressed GAL1) and galactose (transcriptionally active GAL1) growth conditions. Quantitative rtPCR of this cDNA revealed that expression of TAL-PrA did not affect galactose-induced GAL1 transcription (FIG. 7D). To determine whether TAL-PrA enriched chromatin at the GAL1 promoter region, ChIP was performed to the PrA-tag in cells from glucose and galactose growths (FIG. 7E-G). Under transcriptionally active conditions, TAL-PrA specifically enriched chromatin from the GAL1 promoter region relative to sequences 2 kb up- and downstream (FIG. 7F). The level of chromatin enrichment by TAL-PrA under transcriptionally active conditions was similar to the level used for proteomic studies with LexA-PrA affinity enrichment in the ChAP-MS approach (Byrum et al., 2012b). Interestingly, the TAL-PrA protein did not show enrichment of the GAL1 promoter chromatin under transcriptionally repressive glucose growth conditions (FIG. 7G). One possibility of many is that the lack of enrichment could be due to inaccessibility of the TAL-PrA to the genomic target due to altered chromatin structure under transcriptionally repressive conditions—highlighting the importance for measuring specific chromatin enrichment of the TAL protein before using this approach for specific chromatin enrichment. In the previous publication of the ChAP approach (Byrum et al., 2012b), a LexA-PrA was targeted just upstream of the start codon of GAL1 for enrichment of chromatin, which showed enrichment under both glucose and galactose growth conditions. Importantly, the TAL used in the current study was targeted 193 by upstream of the target site of LexA, which suggests that proximal regions may be differentially accessible to DNA-binding affinity reagents under various transcriptional states. In addition to analyzing enrichment of GAL1 chromatin relative to proximal sequences (FIG. 7E-G), enrichment of GAL1 chromatin was measured relative to the five most homologous sequences in the genome (Table 6). The GAL1 target DNA showed 4.6-fold better enrichment relative to the next five most similar sites in the genome—demonstrating specificity of the TAL protein used in this study to the targeted sequence at the GAL1 promoter region. Collectively, the data in FIG. 7C-G and Table 6 demonstrate that the TAL-ChAP-MS approach can provide enriched chromatin from the GAL1 promoter under transcriptionally active conditions that would be suitable for proteomic studies.
Example 5
Using TAL-ChAP-MS to Identify Proteins and Histone PTMs at the GAL1 promoter
As detailed in the Experimental Procedures for Examples 4-5 section, chromatin from the transcriptionally active GAL1 promoter was enriched with TAL-PrA and resolved by SDS-PAGE (FIG. 8A). The similar Coomassie-stained protein pattern for the TAL-PrA and wild-type control samples in FIG. 8A demonstrates that the co-enrichment of contaminating proteins was a major issue for this approach. Accordingly, the label-free spectral counting approach described in the Experimental Procedures for Examples 4-5 section was used to identify proteins specifically enriched with the TAL-PrA. High-resolution mass spectrometry coupled with label-free proteomics was used to identify proteins and histone PTMs specifically enriched with the GAL1 promoter chromatin (FIG. 8B and Table 7). We focused our analysis on the top 10% of enriched proteins (54 proteins) that each showed >15-fold enrichment with the TAL-PrA (Table 7). Four of these 54 proteins (Rpb1, Rpb2, Spt16 and Gal3) are involved with active transcription of GAL1, and these are the same four proteins previously identified at the promoter of GAL1 with the ChAP-MS approach (Byrum et al., 2012b). Rpb1 and Rpb2 are RNA polymerise components, and Spt16 is a subunit of yFACT that aids in re-organizing chromatin for RNA polymerase activity. Gal3 has previously been shown to inhibit the repressive activity of Gal80 at GAL1 locus (Platt and Reece, 1998). Rpb1, Rpb2, Spt16 and Gal3 were confirmed to be associated adjacent to the TAL-PrA genomic binding site with standard ChIP (FIG. 8C). Thus, the TAL-ChAP-MS approach identified precisely the same proteins as the published ChAP-MS approach during transcriptional activation at the promoter of GAL 1, thereby validating the TAL-ChAP-MS approach for studying the local proteome of small chromatin regions and the use of label-free proteomic approaches for quantifying such enrichments. Many of the other 50 proteins identified as >15-fold enriched with TAL-PrA are typical non-specific protein associations found in affinity purifications (e.g. highly abundant metabolic and ribosomal proteins).
In addition to protein associations with the GAL1 promoter, the following single histone PTMs were identified under transcriptionally active conditions: H3K14ac, H3K56ac, H3K79me1/me2/me3, H2BK 17ac and H2AK7ac; and the following combinatorial histone PTMs: H3K9acK14ac, H3K18acK23ac, H2BK6acK11ac and H2BK11acK17ac (FIG. 8B and Table 8). The presence of H3K14ac was confirmed by standard ChIP (FIG. 8C). Previously using ChAP-MS and routine ChIPs (Byrum et al., 2012b), a similar profile of singly acetylated H3 lysine residues was identified at the GAL1 promoter region, thus confirming the utility of the TAL-ChAP-MS approach. In addition to the acetylations observed in the ChAP-MS study, the TAL-ChAP-MS approach additionally identified methylation of H3K79. As previously reported for the ChAP-MS approach, the TAL-ChAP-MS approach uncovered combinatorial sets (i.e. multiple PTMs on single peptides) of histone PTMs under transcriptionally active conditions at the promoter of GAL 1. The use of a technology like TAL-ChAP-MS to identify previously unknown combinatorial modifications is crucial to understand the epigenome, as specific antibodies to combinatorial histone PTMs are not usually available for standard approaches like ChIP. In general terms, acetylation of histone lysine residues and methylation of H3K79 correlate to transcriptional activation (Kouzarides, 2007); thus, the histone PTMs uncovered by TAL-ChAP-MS correlate to the active transcription state of GAL1 in the presence of galactose.
Discussion for Examples 4-5.
We describe a novel approach called TAL-ChAP-MS that provides for the biochemical isolation of 1-kb native chromatin sections for proteomic identification of specifically associated proteins and combinatorial histone PTMs. The described TAL-ChAP-MS approach overcomes limitations of the ChAP-MS approach (Byrum et al., 2012b), as genomic engineering is not necessary for TAL-based affinity enrichment and because protein enrichment with a given locus can now be determined with label-free proteomics. Even without genomic engineering of the DNA, the ChAP-MS approach does require targeting of a DNA-binding affinity enrichment reagent (i.e. the TAL protein), which has the potential to perturb the chromatin state. However, the data in FIG. 7D demonstrate that transcription of GAL1 is not altered on TAL targeting, which supports maintenance of the chromatin integrity for the studies reported here. Targeting TALs to different sequences in adjacent genomic regions that would provide for purification of overlapping chromatin sections is one possible way for investigators to overcome concerns of TAL binding (i.e. a tiling approach). The implications of the TAL-ChAP-MS approach are far-reaching as investigators can now begin to elucidate the dynamics of chromatin regulation in a site-specific and comprehensive manner. Researchers will now only need to ‘reprogram’ the DNA-binding specificity of the TAL protein to obtain a unique affinity purification reagent for their chromosome region of interest. Using the TAL-ChAP-MS approach brings researchers closer to being able to take molecular ‘snapshots’ of the assembly and disassembly of proteins on chromatin and how epigenetic states are modulated at small genomic loci.
Experimental Procedures for Examples 4-5
pTAL-PrA Plasmid, Real-Time rtPCR and ChIP
For affinity enrichment of chromatin from the promoter region of the GAL1 gene in S. cerevisiae, a TAL protein was designed (by the GeneArt Precision TAL services of Life Technologies) to bind a unique 18-nt sequence (GGGGTAATTAATCAGCGA) 193 base pairs upstream of the GAL1 open-reading frame (FIG. 7B). The TAL protein was designed as a truncation that lacked the native N-terminal transcription activation domain, but it contained the site-specific DNA-binding region. To develop an affinity enrichment reagent, the LexA-coding region of pLexA-PrA [plasmid that constitutively expresses a PrA-tagged LexA protein under TRP selection; from (Byrum et al., 2012b)] was replaced with the TAL-coding region to generate pTAL-PrA. Real-time qPCR measurement of galactose-induced transcription of GAL1 and all ChIP studies were performed as reported in (Byrum et al., 2012b).
TAL-ChAP-MS
To test the TAL-ChAP-MS approach at the promoter region of GAL1, wild-type and wild-type (+pTAL-PrA) S. cerevisiae (W303 matA) cells were cultured to mid-log phase in 3% galactose-containing media, subjected to 1.25% formaldehyde cross-linking, cryogenically lysed and subjected to sonication to shear genomic DNA to  ̃1 kb [as detailed in (Byrum et al., 2012b; Byrum et al., 2011a; Byrum et al., 2011b)]. Immunoglobulin G (IgG)-coated Dynabeads were added to lyste from  ̃1011 cells from each growth separately [as detailed in (Byrum et al., 2012b)]. Proteins co-enriching with the TAL-PrA (wild-type cells +pTAL-PrA lysate) or proteins non-specifically binding to the Dynabeads (wild-type cell lysate) were resolved by SDS-PAGE/Coomassie-staining (FIG. 8A), excised as 2-mm bands from the entire gel lane, digested in-gel with trypsin and subjected to high-resolution tandem mass spectrometric analysis with a Thermo Velos Orbitap mass spectrometer [as reported in (Byrum et al., 2012b)]. Proteins and typical histone PTMs (lysine acetylation and methylation) were identified using Mascot (Tables 7 and 8). To measure enrichment of a protein, the normalized spectral abundance factor (Zybailov et al., 2006) was calculated for each protein in each lane by dividing the number of spectral counts (normalized for the size of the protein) of a given protein by the sum of all normalized spectral counts of all proteins in the gel lane (Byrum et al., 2011c). The enrichment level for each protein was identified by calculating the fold enrichment (TAL-PrA/wild type) using the normalized spectral abundance factor values (Table 7). Proteins with a fold enrichment >2 (511 of 1459 proteins identified) were used to generate a quantile plot of fold enrichment with GAL1 promoter chromatin (FIG. 8B).
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TABLE 1





Proteins identified by Mascot Distiller from ChAP-MS analysis of GAL1


chromatin isolated from cells grown in glucose.


Mascot Distiller Quantitation Report







Mascot search results: Glucose










Log ratio versus
Log ratio versus



Intensity
Intensity



(all positive ratios)
(selected ratios)





L/(L + H)
0
0



1.00e+7
5.00e+6



2.00e+7
1.00e+7



3.00e+7
1.50e+7



4.00e+7
2.00e+7 −4 −3



−15 −10 −5 0 5
−2 −1 0 1
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





1
P00925
1180
46885
0.5797
1.009
7










ENO2_YEAST Enolase 2 OS = Saccharomyces cerevisiae GN = ENO2 PE = 1


SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ANLDVKDQK

0.8222
0.03008
0.05098
0.4849
14020.00



2
3
YDLDFKNPES

0.4886
0.04889
0.1516
0.7
2.59E+05





DK









3
2
YDLDFKNPES
X
0.5785
0.01343
0.2062
0.9094
1.62E+05





DK









4
2
AVDDFLLSLD
X
0.5762
0.001
0.2292
0.9942
1.02E+07





GTANK









5
3
AVDDFLLSLD
X
0.5799
0.00158
0.6342
0.9975
8.26E+05





GTANK









6
2
DGKYDLDFK
X
0.5622
0.00842
0.1735
0.989
1.71E+05





NPESDK









7
2
GVMNAVNNV

0.7536
0.05322
0.594
0.4909
2.12E+05





NNVIAAAFVK









8
3
YPIVSIEDPFA
X
0.5768
0
0.8459
0.9995
2.58E+06





EDDWEAWS











HFFK









9
3
RYPIVSIEDPF
X
0.5641
0.0183
0.5271
0.9778
1.27E+05





AEDDWEAW











SHFFK









10 
3
YGASAGNVG
X
0.5825
0
0.9229
0.9993
1.78E+07





DEGGVAPNI











QTAEEALDLI











VDAIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





2
P00924
1117
46773
0.5798
1.008
5










ENO1_YEAST Enolase 1 OS = Saccharomyces cerevisiae GN = ENO1 PE = 1


SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ANIDVKDQK

0.8222
0.03008
0.05098
0.4849
1.40E+04



2
2
AVDDFLISLD
X
0.5762
0.001
0.2292
0.9942
1.02E+07





GTANK









3
3
AVDDFLISLD
X
0.5799
0.00158
0.6342
0.9975
8.26E+05





GTANK









4
3
IEEELGDNAV
X
0.6064
0.00518
0.5017
0.978
3.82E+05





FAGENFHHG











DKL









5
3
YPIVSIEDPFA
X
0.5768
0
0.8459
0.9995
2.58E+06





EDDWEAWS











HFFK









6
3
RYPIVSIEDPF
X
0.5641
0.0183
0.5271
0.9778
1.27E+05





AEDDWEAW











SHFFK









7
3
YGASAGNVG
X
0.5825
0
0.9229
0.9993
1.78E+07





DEGGVAPNI











QTAEEALDLI











VDAIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





3
P10592
565
69844
0.5495

10










HSP72_YEAST Heat shock protein SSA2 OS = Saccharomyces cerevisiae


GN = SSA2 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ITITNDKGR
X
0.9873
0.0152
0.06237
0.9611
4.21E+04



2
2
NFNDPEVQG
X
0.554
0.0076
0.3809
0.9603
8.52E+05





DMK









3
2
FKEEDEKESQR
X
0.5702
0.0088
0.0696
0.9865
9.27E+04



4
2
NFTPEQISSM
X
0.5605
0.00872
0.1288
0.9508
5.66E+05





VLGK









5
2
LIDVDGKPQI
X
0.5488
0.00255
0.256
0.9909
4.00E+05





QVEFK









6
3
LIDVDGKPQI
X
0.5555
0.00158
0.624
0.9945
2.37E+06





QVEFK









7
3
IINEPTAAAIA
X
0.5399
0.00584
0.05784
0.938
3.22E+05





YGLDKK









8
3
LDKSQVDEIV
X
0.528
0.02077
0.3666
0.7616
7.53E+05





LVGGSTR









9
3
NTISEAGDKL
X
0.5444
0.00255
0.3405
0.9868
2.60E+06





EQADKDAVTK









10 
3
TQDLLLLDVA
X
0.5041
0.07248
0.196
0.9741
1.75E+05





PLSLGIETAG











GVMTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





4
P06169
555
61737
0.5581
1.008
5










PDC1_YEAST Pyruvate decarboxylase isozyme 1 OS = Saccharomyces


cerevisiae GN = PDC1 PE = 1 SV = 7

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
NATFPGVQMK
X
0.5499
0.00466
0.3978
0.9842
1.13E+06



2
3
VATTGEWDK
X
0.5476
0.00455
0.265
0.9899
1.17E+06





LTQDK









3
3
LLQTPIDMSL
X
0.5635
0.00264
0.4617
0.9956
2.39E+05





KPNDAESEK









4
2
MIEIMLPVFD
X
0.5603
0.0038
0.7877
0.9907
7.07E+06





APQNLVEQAK









5
3
LLQTPIDMSL
X
0.56
0.00158
0.5686
0.9967
2.71E+06





KPNDAESEKE











VIDTILALVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





5
P10591
551
70039
0.5549

9










HSP71_YEAST Heat shock protein SSA1 OS = Saccharomyces cerevisiae


GN = SSA1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ITITNDKGR
X
0.9873
0.0152
0.06237
0.9611
4.21E+04



2
2
NFNDPEVQA
X
0.595
0.00755
0.1662
0.9451
4.27E+05





DMK









3
2
FKEEDEKESQR
X
0.5702
0.0088
0.0696
0.9865
9.27E+04



4
2
NFTPEQISSM
X
0.5605
0.00872
0.1288
0.9508
5.66E+05





VLGK









5
2
LIDVDGKPQI
X
0.5488
0.00255
0.256
0.9909
4.00E+05





QVEFK









6
3
LIDVDGKPQI
X
0.5555
0.00158
0.624
0.9945
2.37E+06





QVEFK









7
3
IINEPTAAAIA
X
0.5399
0.00584
0.05784
0.938
3.22E+05





YGLDKK









8
3
LDKSQVDEIV
X
0.528
0.02077
0.3666
0.7616
7.53E+05





LVGGSTR









9
3
TQDLLLLDVA
X
0.5041
0.07248
0.196
0.9741
1.75E+05





PLSLGIETAG











GVMTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





6
P15108
548
80850
0.4277

10










HSC82_YEAST ATP-dependent molecular chaperone HSC82


OS = Saccharomyces cerevisiae GN = HSC82 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SPFLDALK
X
0.594
0.00899
0.5359
0.9605
4.97E+05



2
3
ALKDILGDQV
X
0.5513
0.02217
0.189
0.9214
5.90E+04





EK









3
3
VKEEVQELEE
X
0.5794
0.01043
0.07342
0.9201
7.47E+04





LNK









4
2
LEEVDEEEEE

0.1049
999
0.1111
0.1643
2.69E+04





KKPK









5
2
LFLKDDQLEY
X
0.5684
0.02513
0.191
0.9399
5.88E+05





LEEK









6
3
LFLKDDQLEY
X
0.4997
0.04689
0.1356
0.8192
3.36E+05





LEEKR









7
3
TLVDITKDFE
X
0.4212
0.04847
0.09843
0.7318
2.17E+05





LEETDEEK









8
2
VFITDEAEDLI
X
0.5569
0.00991
0.227
0.9585
1.35E+06





PEWLSFVK









9
3
VFITDEAEDLI
X
0.5764
0.00772
0.5192
0.9965
3.80E+05





PEWLSFVK









10 
3
RVFITDEAED
X
0.5766
0.02142
0.2893
0.9293
1.19E+05





LIPEWLSFVK









11 
3
TLVDITKDFE
X
0.216
0.1336
0.2606
0.801
1.35E+06





LEETDEEKAER
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





7
P00560
506
44711
0.5584

4










PGK_YEAST Phosphoglycerate kinase OS = Saccharomyces cerevisiae


GN = PGK1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
VDFNVPLDG
X
0.3003
0.01134
0.1059
0.8842
3.08E+05





KK









2
2
VLENTEIGDS

0.9928
0.00158
0.8106
0.3129
3.18E+07





IFDK









3
2
SSAAGNTVII
X
0.577
0.00158
0.6503
0.9976
1.77E+06





GGGDTATVAK









4
3
GVEVVLPVDF
X
0.6021
0.00634
0.4734
0.9828
1.32E+06





IIADAFSADA











NTK









5
2
GVEVVLPVDF
X
0.5722
0.00525
0.5529
0.9973
1.42E+06





IIADAFSADA











NTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





8
P00359
492
35724
0.5592
1.017
5










G3P3_YEAST Glyceraldehyde-3-phosphate dehydrogenase 3


OS = Saccharomyces cerevisiae GN = TDH3 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ELDTAQK
X
0.5482
0.00832
0.1767
0.9264
2.25E+04



2
2
VVDLVEHVAK
X
0.5557
0.001
0.6963
0.9976
2.33E+06



3
2
YAGEVSHDDK

0.7269
0.01789
0.2422
0.6988
8.10E+04



4
2
TASGNIIPSS
X
0.5621
0.00158
0.7985
0.9966
9.13E+06





TGAAK









5
3
VPTVDVSVV
X
0.5299
0.00836
0.3828
0.9782
2.33E+05





DLTVK









6
3
YAGEVSHDD

0.4138
0.03022
0.1569
0.4338
1.27E+06





KHIIVDGK









7
2
YAGEVSHDD

0.4604
0.01421
0.386
0.4585
4.81E+05





KHIIVDGK









8
2
DPANLPWGS
X
0.5497
0.00466
0.5417
0.9953
1.10E+06





SNVDIAIDST











GVFK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





9
P00950
289
27592
0.5753
1.028
4










PMG1_YEAST Phosphoglycerate mutase 1 OS = Saccharomyces cerevisiae


GN = GPM1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
KVYPDVLYTSK
X
0.6133
0.00839
0.05839
0.9039
9.79E+04



2
2
LLPYWQDVIAK
X
0.5686
0.001
0.6124
0.9984
3.23E+06



3
2
SFDVPPPPID
X
0.579
0.00467
0.7461
0.9747
5.95E+06





ASSPFSQK









4
3
RSFDVPPPPI
X
0.5607
0.0055
0.1214
0.9811
2.74E+05





DASSPFSQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





10
P00942
273
26779
0.8938
1.241
4










TPIS_YEAST Triosephosphate isomerase OS = Saccharomyces cerevisiae


GN = TPI1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
KPQVTVGAQ
X
1
0
0.6505
0.7407
2.01E+06





NAYLK









2
2
ASGAFTGEN
X
0.8721
0.00784
0.8579
0.9988
1.90E+06





SVDQIK









3
3
SYFHEDDKFI
X
0.5635
0.00564
0.2565
0.9791
2.28E+05





ADK









4
2
ASGAFTGEN
X
0.5037
0.05902
0.5738
0.8696
1.28E+05





SVDQIKDVG











AK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





11
P23254
258
74104
0.5924
1.089
4










TKT1_YEAST Transketolase 1 OS = Saccharomyces cerevisiae GN = TKL1


PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LFSEYQK

0.7783
0.02398
0.136
0.6468
1.69E+05



2
2
ILAVDTVSK
X
0.6661
0.02039
0.1191
0.8514
6.18E+05



3
3
KFPELGAELAR
X
0.4889
0.01828
0.08146
0.9458
3.41E+04



4
2
LSGQLPANW

0.9991
0.00158
0.5921
0.6509
1.69E+06





ESK









5
2
VVSLPDFFTF
X
0.5277
0.01746
0.3974
0.82
4.93E+05





DK









6
2
QNLPQLEGS
X
0.5395
0.00842
0.1282
0.9767
9.63E+04





SIESASK









7
2
SFVVPQEVYD

0.4152
0.04681
0.3912
0.41
1.50E+05





HYQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





12
P34760
251
21688
0.5583

1










TSA1_YEAST Peroxiredoxin TSA1 OS = Saccharomyces cerevisiae


GN = TSA1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TAVVDGVFD
X
0.5583
0.01341
0.4102
0.9415
7.29E+05





EVSLDK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





13
P02994
242
50001
0.5996

5










EF1A_YEAST Elongation factor 1-alpha OS = Saccharomyces cerevisiae


GN = TEF1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
FQEIVK
X
0.9909
0.00329
0.1232
0.9948
5.97E+05



2
2
LPLQDVYK
X
0.5266
0.002
0.5985
0.9845
4.55E+06



3
3
SHINVVVIGH
X
0.5427
0.01093
0.07069
0.9813
4.33E+04





VDSGK









4
3
TLLEAIDAIEQ
X
0.6222
0.01
0.3809
0.7963
1.58E+07





PSRPTDKPLR









5
3
SVEMHHEQL
X
0.5271
0.00255
0.8205
0.9972
2.24E+06





EQGVPGDNV











GFNVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





14
P11484
235
66937
0.5697
1.042
3










HSP75_YEAST Heat shock protein SSB1 OS = Saccharomyces cerevisiae


GN = SSB1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LLSDFFDGK
X
0.5313
0.004
0.3939
0.9936
1.18E+06



2
2
VIDVDGNPVI
X
0.5573
0.03139
0.2885
0.9312
2.81E+05





EVQYLEETK









3
3
STSGNTHLG
X
0.6018
0.01912
0.5754
0.975
1.64E+06





GQDFDTNLLE











HFK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





15
P16521
220
115920
0.4751
1.086
3










EF3A_YEAST Elongation factor 3A OS = Saccharomyces cerevisiae


GN = YEF3 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
QINENDAEA
X
0.502
0.03789
0.1931
0.9204
1.87E+05





MNK









2
2
ATETVDNKDI
X
0.5572
0.01016
0.3336
0.9535
2.92E+05





ER









3
2
LVEDPQVIAP
X
0.4314
0.01731
0.1193
0.9722
5.89E+05





FLGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





16
P14540
217
39812
0.5455
1.017
4










ALF_YEAST Fructose-bisphosphate aldolase OS = Saccharomyces


cerevisiae GN = FBA1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LLPWFDGML
X
0.5387
0.01791
0.6343
0.9901
2.73E+06





EADEAYFK









2
3
LLPWFDGML
X
0.5693
0.00324
0.7442
0.9942
4.58E+05





EADEAYFK









3
2
KLLPWFDGM
X
0.5497
0.02627
0.3049
0.8469
4.81E+04





LEADEAYFK









4
3
KLLPWFDGM
X
0.5579
0.00588
0.6699
0.9919
6.41E+05





LEADEAYFK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





17
P05750
214
26630
0.5144

1










RS3_YEAST 40S ribosomal protein S3 OS = Saccharomyces cerevisiae


GN = RPS3 PE = 1 SV = 5

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
ALPDAVTIIEP
X
0.5144
0.00787
0.0782
0.9853
1.22E+06





KEEEPILAPS











VK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





18
P38788
196
58515
0.5268
1.003
2










SSZ1_YEAST Ribosome-associated complex subunit SSZ1


OS = Saccharomyces cerevisiae GN = SSZ1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EAVLTVPTNF
X
0.5251
0.00574
0.2728
0.9966
3.66E+05





SEEQK









2
3
LISDYDADEL
X
0.5276
0.00557
0.6012
0.9986
7.77E+05





AEALQPVIVN











TPHLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





19
P40150
195
66930
0.5697
1.042
3










HSP76_YEAST Heat shock protein SSB2 OS = Saccharomyces cerevisiae


GN = SSB2 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LLSDFFDGK
X
0.5313
0.004
0.3939
0.9936
1.18E+06



2
2
VIDVDGNPVI
X
0.5573
0.03139
0.2885
0.9312
2.81E+05





EVQYLEETK









3
3
STSGNTHLG
X
0.6018
0.01912
0.5754
0.975
1.64E+06





GQDFDTNLLE











HFK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





20
P32324
189
93719
0.4948
1.141
4










EF2_YEAST Elongation factor 2 OS = Saccharomyces cerevisiae GN = EFT1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TGTLTTSETA
X
0.5494
0.05488
0.2574
0.9685
3.09E+04





HNMK









2
2
ETVESESSQT
X
0.4964
0.00945
0.5999
0.989
1.00E+06





ALSK









3
3
WTNKDTDAE
X
0.4881
0.01896
0.04008
0.9109
1.19E+05





GKPLER









4
2
WTNKDTDAE
X
0.383
0.06499
0.03736
0.93
1.87E+04





GKPLER
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





21
P32589
184
77318


0










HSP7F_YEAST Heat shock protein homolog SSE1 OS = Saccharomyces


cerevisiae GN = SSE1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
QVEDEDHME

0.6809
0.02791
0.3031
0.3098
9.21E+05





VFPAGSSFPS











TK









2
3
QSISEAFGKP

0.5365
0.06281
0.4112
0.2745
3.29E+05





LSTTLNQDEA











IAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





22
P54115
183
54380
0.6157

1










ALDH6_YEAST Magnesium-activated aldehyde dehydrogenase, cytosolic


OS = Saccharomyces cerevisiae GN = ALD6 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SAHLVFDDA
X
0.6157
0.0168
0.06354
0.9683
1.83E+04





NIKK









2
3
IVKEEIFGPV

−0.01367
0.6603
0.692
0.03687
2.37E+06





VTVAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





23
P00360
179
35728
0.5624
1.059
4










G3P1_YEAST Glyceraldehyde-3-phosphate dehydrogenase 1


OS = Saccharomyces cerevisiae GN = TDH1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ELDTAQK
X
0.5482
0.00832
0.1767
0.9264
2.25E+04



2
2
TASGNIIPSS
X
0.5621
0.00158
0.7985
0.9966
9.13E+06





TGAAK









3
3
VPTVDVSVV
X
0.5299
0.00836
0.3828
0.9782
2.33E+05





DLTVK









4
3
IATYQERDPA
X
0.6109
0.00894
0.4762
0.9875
2.36E+05





NLPWGSLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





24
P05694
159
86296
0.5474
1.143
4










METE_YEAST 5-methyltetrahydropteroyltriglutamate--homocysteine


methyltransferase OS = Saccharomyces cerevisiae GN = MET6 PE = 1


SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VATSGVANK
X
0.4292
0.05981
0.2367
0.7626
5.78E+05



2
2
ITVDELFK
X
0.7613
0.02167
0.4122
0.9349
3.00E+05



3
2
ALDADVVSIE
X
0.5995
0.00506
0.3617
0.9908
4.15E+05





FSK









4
3
APEQFDEVVA
X
0.5769
0.02178
0.2145
0.9228
7.39E+04





AIGNK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





25
P00817
159
32280
0.3148
1.707
2










IPYR_YEAST Inorganic pyrophosphatase OS = Saccharomyces cerevisiae


GN = IPP1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LNDIEDVEK
X
0.1915
0.08967
0.192
0.967
2.15E+05



2
3
LEITKEETLNP

0.5691
0.01513
0.1321
0.6614
3.55E+04





IIQDTKK









3
3
AVGDNDPID
X
0.5565
0.00915
0.5386
0.9951
1.89E+05





VLEIGETIAYT











GQVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





26
P46655
156
81369
0.4215
1.269
2










SYEC_YEAST Glutamyl-tRNA synthetase cytoplasmic


OS = Saccharomyces cerevisiae GN = GUS1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
KNDDGSMVAK
X
0.5902
0.05607
0.0228
0.8152
515.7



2
3
EKEEFQDSIL
X
0.4214
0.04183
0.2818
0.7588
6.23E+05





EDLDLLGIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





27
P09436
156
123651
0.9973

1










SYIC_YEAST Isoleucyl-tRNA synthetase, cytoplasmic


OS = Saccharomyces cerevisiae GN = ILS1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
MSNIDFQYD
X
0.9973
0.00158
0.6248
0.961
3.01E+06





DSVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





28
P61864
148
8552
0.8538

1










UBIQ_YEAST Ubiquitin OS = Saccharomyces cerevisiae GN = UBI1 PE = 1


SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IQDKEGIPPD
X
0.8538
0.01276
0.1534
0.8756
1.67E+05





QQR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





29
P04456
146
15748
0.5126

1










RL25_YEAST 60S ribosomal protein L25 OS = Saccharomyces cerevisiae


GN = RPL25 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ELYEVDVLK
X
0.5126
0.00785
0.1734
0.9804
4.97E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





30
P12709
146
61261
0.5947

3










G6PI_YEAST Glucose-6-phosphate isomerase OS = Saccharomyces


cerevisiae GN = PGI1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
NWFLSK
X
0.5893
0.01445
0.08506
0.8965
1.22E+04



2
2
TFTTAETITN

0.7863
0.02669
0.2797
0.4859
1.42E+05





ANTAK









3
2
NLVNDEIIAA
X
0.7445
0.01763
0.05341
0.9308
1.58E+04





LIELAK









4
3
ANKPMYVDG
X
0.5898
0.03119
0.315
0.7014
4.18E+05





VNVAPEVDS











VLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





31
P08524
145
40738
0.5181

1










FPPS_YEAST Farnesyl pyrophosphate synthase OS = Saccharomyces


cerevisiae GN = FPP1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TVEQLGQEEY
X
0.5181
0.00585
0.1843
0.9906
4.80E+05





EK









2
2
IEQLYHEYEE

0.3587
0.08308
0.1586
0.6297
6.38E+04





SIAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





32
P00330
142
36800
0.5295
1.039
3










ADH1_YEAST Alcohol dehydrogenase 1 OS = Saccharomyces cerevisiae


GN = ADH1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ANELLINVK
X
0.5781
0.01445
0.406
0.9865
4.01E+05



2
2
VVGLSTLPEI
X
0.518
0.001
0.6074
0.9963
5.17E+06





YEK









3
3
VLGIDGGEG
X
0.5414
0.00403
0.7131
0.9802
3.52E+06





KEELFR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





33
P07262
138
49763
0.2171

1










DHE4_YEAST NADP-specific glutamate dehydrogenase 1


OS = Saccharomyces cerevisiae GN = GDH1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
VTWENDKGE
X
0.2171
0.1184
0.5086
0.7666
6.81E+05





QEVAQGYR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





34
P31373
138
42692
0.6023
1.05
2










CYS3_YEAST Cystathionine gamma-lyase OS = Saccharomyces cerevisiae


GN = CYS3 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ISVGIEDTDD
X
0.613
0.00887
0.1862
0.967
6.82E+05





LLEDIK









2
3
ISVGIEDTDD
X
0.5634
0.01345
0.3481
0.9112
1.80E+05





LLEDIKQALK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





35
P22202
137
70009
0.5832
1.457
2










HSP74_YEAST Heat shock protein SSA4 OS = Saccharomyces cerevisiae


GN = SSA4 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ITITNDKGR
X
0.9873
0.0152
0.06237
0.9611
4.21E+04



2
3
IINEPTAAAIA
X
0.5399
0.00584
0.05784
0.938
3.22E+05





YGLDKK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





36
A6ZP47
134
65697
0.3172

1










DED1_YEAS7 ATP-dependent RNA helicase DED1 OS = Saccharomyces


cerevisiae (strain YJM789) GN = DED1 PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TGGFLFPVLS
X
0.3172
0.03297
0.08265
0.8019
3.08E+05





ESFK









2
3
DVPEPITEFT

0.00052
7.122
0.6671
0.1659
1.16E+06





SPPLDGLLLE











NIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





37
P00549
134
54510
0.5402
2.375
2










KPYK1_YEAST Pyruvate kinase 1 OS = Saccharomyces cerevisiae


GN = PYK1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EVLGEQGKD

0.8211
0.01418
0.5587
0.4163
9.19E+05





VK









2
3
MNFSHGSYE
X
0.159
0.3656
0.233
0.8491
3.57E+04





YHK









3
3
GVNLPGTDV
X
0.5499
0.00705
0.3217
0.9634
2.45E+06





DLPALSEKDK











EDLR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





38
P29311
134
30073
0.5686
1.063
3










BMH1_YEAST Protein BMH1 OS = Saccharomyces cerevisiae GN = BMH1


PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
LAEQAERYEE
X
0.6493
0.01923
0.1302
0.8619
2.33E+04





MVENMK









2
3
QAFDDAIAEL
X
0.5798
0.00382
0.3875
0.9933
2.42E+05





DTLSEESYK









3
3
ISDDILSVLD
X
0.5643
0.01199
0.1289
0.8075
1.04E+06





SHLIPSATTG











ESK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





39
P26321
133
33890


0










RL5_YEAST 60S ribosomal protein L5 OS = Saccharomyces cerevisiae


GN = RPL5 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





40
P26263
130
61542


0










PDC6_YEAST Pyruvate decarboxylase isozyme 3 OS = Saccharomyces


cerevisiae GN = PDC6 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





41
A6ZQJ1
121
44837
0.5295

1










IF4A_YEAS7 ATP-dependent RNA helicase eIF4A OS = Saccharomyces


cerevisiae (strain YJM789) GN = TIF1 PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
AIMPIIEGHD
X
0.5295
0.00498
0.5721
0.9845
4.30E+05





VLAQAQSGT











GK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





42
Q02753
119
18231
0.4842

1










RL21A_YEAST 60S ribosomal protein L21-A OS = Saccharomyces


cerevisiae GN = RPL21A PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VGDIVDIK
X
0.4842
0.00614
0.01566
0.9582
1.27E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





43
P05030
119
99941
0.5928

1










PMA1_YEAST Plasma membrane ATPase 1 OS = Saccharomyces


cerevisiae GN = PMA1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
TVEEDHPIPE
X
0.5928
0.02245
0.3764
0.8651
3.27E+05





DVHENYENK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





44
Q03195
119
68297


0










RLI1_YEAST Translation initiation factor RLI1 OS = Saccharomyces


cerevisiae GN = RLI1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
LLAGALKPDE

0.1154
0.2281
0.1563
0.679
1.09E+05





GQDIPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





45
P38011
119
34936
0.4788

1










GBLP_YEAST Guanine nucleotide-binding protein subunit beta-like


protein OS = Saccharomyces cerevisiae GN = ASC1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
VVPNEKADD
X
0.4788
0.00934
0.03497
0.9434
2.43E+05





DSVTIISAGN











DK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





46
P19097
117
206818
0.6972

1










FAS2_YEAST Fatty acid synthase subunit alpha OS = Saccharomyces


cerevisiae GN = FAS2 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EIYYTPDPSEL
X
0.6972
0.02896
0.2436
0.8764
4.39E+05





AAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





47
P22768
116
47175


0










ASSY_YEAST Argininosuccinate synthase OS = Saccharomyces cerevisiae


GN = ARG1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





48
P41277
112
28138
0.5193
1.003
2










GPP1_YEAST (DL)-glycerol-3-phosphatase 1 OS = Saccharomyces


cerevisiae GN = GPP1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
FAPDFADEEY

0.2622
0.08634
0.2384
0.6536
3.56E+05





VNK









2
3
FAPDFADEEY
X
0.5189
0.00547
0.2526
0.9631
1.44E+06





VNKLEGEIPEK









3
2
VGEYNAETDE
X
0.5217
0.01439
0.5462
0.9935
2.38E+05





VELIFDDYLY











AK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





49
P49090
110
64857
0.5527
1.053
2










ASNS2_YEAST Asparagine synthetase [glutamine-hydrolyzing] 2


OS = Saccharomyces cerevisiae GN = ASN2 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
YFTPDWLDEK
X
0.5819
0.02038
0.1065
0.9343
3.09E+05



2
3
AFDTTDEPDV
X
0.5251
0.03417
0.2562
0.9393
3.11E+05





KPYLPEEILWR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





50
P15624
110
67691
0.9837
1.076
3










SYFB_YEAST Phenylalanyl-tRNA synthetase beta chain


OS = Saccharomyces cerevisiae GN = FRS1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SKEGAEPK
X
0.9916
0.00141
0.07152
0.9856
1.79E+06



2
2
GYWIEEDDS
X
0.8641
0.05554
0.05094
0.8192
3.24E+04





VK









3
2
NSGFEIIQGL
X
0.8704
0.03036
0.142
0.8105
8.54E+04





LGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





51
P19882
109
60714
0.4595

1










HSP6O_YEAST Heat shock protein 60, mitochondrial OS = Saccharomyces


cerevisiae GN = HSP60 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
NVLIEQPFGP

0.3833
0.07553
0.1289
0.6499
8.66E+04





PK









2
2
AAVEEGILPG
X
0.4595
0.03115
0.1117
0.9559
1.38E+05





GGTALVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





52
P38088
109
75845


0










SYG_YEAST Glycyl-tRNA synthetase 1 OS = Saccharomyces cerevisiae


GN = GRS1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





53
P07284
105
53276


0










SYSC_YEAST Seryl-tRNA synthetase, cytoplasmic OS = Saccharomyces


cerevisiae GN = SES1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





54
P53184
99
24978
0.4323

1










PNC1_YEAST Nicotinamidase OS = Saccharomyces cerevisiae GN = PNC1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
TTVLLDYTRPI
X
0.4323
0.02539
0.2814
0.7218
1.46E+06





SDDPEVINK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





55
P36008
99
46827
0.8918
1.457
2










EF1G2_YEAST Elongation factor 1-gamma 2 OS = Saccharomyces


cerevisiae GN = TEF4 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LLGSDVIEK
X
0.9663
0.00996
0.4982
0.9961
1.44E+06



2
2
WFNTVAASPI
X
0.527
0.01203
0.07669
0.8876
2.21E+05





VK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





56
Q01560
95
45444


0










NOP3_YEAST Nucleolar protein 3 OS = Saccharomyces cerevisiae


GN = NPL3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





57
P40213
94
15974


0










RS16_YEAST 40S ribosomal protein S16 OS = Saccharomyces cerevisiae


GN = RPS16A PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
YVDEQSKNE

0.9917
0.00434
0.3579
0.08027
4.77E+05





LK









2
2
YVDEQSKNE

0.9999
0.00574
0.1204
0.1164
4.58E+05





LKK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





58
P16140
94
57922


0










VATB_YEAST V-type proton ATPase subunit B OS = Saccharomyces


cerevisiae GN = VMA2 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





59
P25293
93
47855
0.5024

1










NAP1_YEAST Nucleosome assembly protein OS = Saccharomyces


cerevisiae GN = NAP1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LGSLVGQDS
X
0.5024
0.03188
0.08129
0.758
2.53E+04





GYVGGLPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





60
P41940
93
39781
0.5624
1.009
2










MPG1_YEAST Mannose-1-phosphate guanyltransferase


OS = Saccharomyces cerevisiae GN = MPG1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LATGANIVGN
X
0.5695
0.00687
0.05507
0.9887
2.54E+04





ALIDPTAK









2
3
INAGLYILNPE
X
0.562
0.00414
0.5133
0.9966
4.50E+05





VIDLIEMKPT











SIEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





61
P15705
93
66705


0










STI1_YEAST Heat shock protein STI1 OS = Saccharomyces cerevisiae


GN = STI1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





62
Q03048
91
15979


0










COFI_YEAST Cofilin OS = Saccharomyces cerevisiae GN = COF1 PE = 1


SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SGVAVADES

0.2984
0.1196
0.0948
0.4874
1.00E+05





LTAFNDLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





63
P38707
90
62168
0.6442

1










SYNC_YEAST Asparaginyl-tRNA synthetase, cytoplasmic


OS = Saccharomyces cerevisiae GN = DED81 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SVQYVLEDPI
X
0.6442
0.02511
0.182
0.8768
2.97E+05





AGPLVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





64
P49089
89
64734
0.4454
1.252
2










ASNS1_YEAST Asparagine synthetase [glutamine-hydrolyzing] 1


OS = Saccharomyces cerevisiae GN = ASN1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
YFTPDWLDEK
X
0.5819
0.02038
0.1065
0.9343
3.09E+05



2
2
ATNDVEPSTY
X
0.375
0.01032
0.3126
0.9726
4.80E+05





DSK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





65
P14832
88
17380


0










CYPH_YEAST Peptidyl-prolyl cis-trans isomerase OS = Saccharomyces


cerevisiae GN = CPR1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
KVESLGSPSG

0.5598
0.00415
0.2553
0.5249
4.83E+05





ATK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





66
P0C0W9
86
19844
0.3135

1










RL11A_YEAST 60S ribosomal protein L11-A OS = Saccharomyces


cerevisiae GN = RPL11A PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VLEQLSGQTP

0.000776
0.4364
0.8707
0.2733
1.50E+07





VQSK









2
3
VLEQLSGQTP
X
0.3135
0.169
0.1611
0.8233
1.39E+04





VQSK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





67
P14120
84
11504
0.5841

1










RL30_YEAST 60S ribosomal protein L30 OS = Saccharomyces cerevisiae


GN = RPL30 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VYYFQGGNN
X
0.5841
0.02582
0.205
0.8988
9.20E+04





ELGTAVGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





68
P26755
84
13863


0










RFA3_YEAST Replication factor A protein 3 OS = Saccharomyces


cerevisiae GN = RFA3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





69
P04147
83
64304


0










PABP_YEAST Polyadenylate-binding protein, cytoplasmic and nuclear


OS = Saccharomyces cerevisiae GN = PAB1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TAEQLENLNI

0.001099
1.859
0.4682
0.9671
3.84E+05





QDDQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





70
P32527
82
49439


0










ZUO1_YEAST Zuotin OS = Saccharomyces cerevisiae GN = ZUO1 PE = 1


SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





71
P38625
82
58750
0.5454

1










GUAA_YEAST GMP synthase [glutamine-hydrolyzing]


OS = Saccharomyces cerevisiae GN = GUA1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VTYDITSKPP
X
0.5454
0.01078
0.239
0.9456
3.32E+05





ATVEWE
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





72
P31412
80
44434
0.6452

1










VATC_YEAST V-type proton ATPase subunit C OS = Saccharomyces


cerevisiae GN = VMA5 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IGSLDTLIVE
X
0.6452
0.01519
0.07177
0.9753
2.77E+04





SEELSK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





73
P05753
80
29608


0










RS4_YEAST 40S ribosomal protein S4 OS = Saccharomyces cerevisiae


GN = RPS4A PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





74
P26783
79
25023
0.4952

1










RS5_YEAST 40S ribosomal protein S5 OS = Saccharomyces cerevisiae


GN = RPS5 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
TIAETLAEELI
X
0.4952
0.0071
0.5691
0.9574
1.53E+05





NAAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





75
P17076
76
28396


0










RL8A_YEAST 60S ribosomal protein L8-A OS = Saccharomyces cerevisiae


GN = RPL8A PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





76
P53030
76
24470
0.5139

1










RL1_YEAST 60S ribosomal protein L1 OS = Saccharomyces cerevisiae


GN = RPL1A PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
FPTPVSHND
X
0.5139
0.02598
0.07442
0.8939
3.55E+05





DLYGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





77
P25694
74
92331
0.5765

1










CDC48_YEAST Cell division control protein 48 OS = Saccharomyces


cerevisiae GN = CDC48 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
AAAPTVVFLD
X
0.5765
0.01988
0.2107
0.9888
1.27E+05





ELDSIAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





78
P40303
73
28574


0










PSA7_YEAST Proteasome component PRE6 OS = Saccharomyces


cerevisiae GN = PRE6 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





79
P16861
73
108408


0










K6PF1_YEAST 6-phosphofructokinase subunit alpha OS = Saccharomyces


cerevisiae GN = PFK1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





80
P35691
73
18729


0










TCTP_YEAST Translationally-controlled tumor protein homolog


OS = Saccharomyces cerevisiae GN = TMA19 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LQETNPEEVP

0.01574
0.05686
0.3046
0.3037
2.21E+06





KFEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





81
P05738
72
21556
0.6443

1










RL9A_YEAST 60S ribosomal protein L9-A OS = Saccharomyces cerevisiae


GN = RPL9A PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
FLDGIYVSHK
X
0.6443
0.01495
0.1913
0.8882
2.99E+04



2
3
YIQTEQQIEV

0.008727
0.6329
0.355
0.4397
1.88E+06





PEGVTVSIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





82
P00899
71
56732


0










TRPE_YEAST Anthranilate synthase component 1 OS = Saccharomyces


cerevisiae GN = TRP2 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





83
P17079
71
17956
0.5847

1










RL12_YEAST 60S ribosomal protein L12 OS = Saccharomyces cerevisiae


GN = RPL12A PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
VDFKNPHDII
X
0.5847
0.02535
0.1429
0.8697
3.12E+05





EGINAGEIEIP











EN
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





84
P07806
70
126596
0.4001
1.235
2










SYV_YEAST Valyl-tRNA synthetase, mitochondrial OS = Saccharomyces


cerevisiae GN = VAS1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TGVFEPEFTA
X
0.365
0.03845
0.2789
0.8561
4.52E+05





DGK









2
2
LNTAISNLEV
X
0.5312
0.02003
0.0767
0.9905
1.46E+05





ENK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





85
P26781
70
17898
0.4992

1










RS11_YEAST 40S ribosomal protein S11 OS = Saccharomyces cerevisiae


GN = RPS11A PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TAIEGSYIDKK
X
0.4992
0.0041
0.1365
0.9905
1.73E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





86
P53252
70
38326
0.5822

1










PIL1_YEAST Sphingolipid long chain base-responsive protein PIL1


OS = Saccharomyces cerevisiae GN = PIL1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
APTASQLQNP
X
0.5822
0.02737
0.2412
0.8526
1.83E+04





PPPPSTTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





87
P22943
68
11686


0










HSP12_YEAST 12 kDa heat shock protein OS = Saccharomyces cerevisiae


GN = HSP12 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GKDNAEGQG

0.01324
0.7291
0.2434
0.4791
3.47E+04





ESLADQAR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





88
P02407
67
15891


0










RS17A_YEAST 40S ribosomal protein S17-A OS = Saccharomyces


cerevisiae GN = RPS17A PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





89
P04801
66
84467


0










SYTC_YEAST Threonyl-tRNA synthetase, cytoplasmic


OS = Saccharomyces cerevisiae GN = THS1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TVSQADFPGL

0.9625
0.01322
0.639
0.3281
3.05E+05





EGVAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





90
P09733
63
49945


0










TBA1_YEAST Tubulin alpha-1 chain OS = Saccharomyces cerevisiae


GN = TUB1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





91
P33204
62
19959


0










ARPC4_YEAST Actin-related protein 2/3 complex subunit 4


OS = Saccharomyces cerevisiae GN = ARC19 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





92
P23301
62
17208
0.4447

1










IF5A2_YEAST Eukaryotic translation initiation factor 5A-2


OS = Saccharomyces cerevisiae GN = HYP2 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
KLEDLSPSTH
X
0.4447
0.02507
0.3275
0.7978
8.63E+05





NMEVPVVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





93
P06168
61
44565


0










ILV5_YEAST Ketol-acid reductoisomerase, mitochondrial


OS = Saccharomyces cerevisiae GN = ILV5 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





94
P05744
59
12219
0.6527

1










RL33A_YEAST 60S ribosomal protein L33-A OS = Saccharomyces


cerevisiae GN = RPL33A PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IEGVATPQDA
X
0.6527
0.01745
0.2096
0.9659
1.36E+05





QFYLGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





95
P04807
58
53908
0.6227

1










HXKB_YEAST Hexokinase-2 OS = Saccharomyces cerevisiae GN = HXK2


PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
TKYDITIDEE
X
0.6227
0.02524
0.2555
0.8918
7.65E+04





SPRPGQQTFEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





96
P03965
58
124439


0










CARB_YEAST Carbamoyl-phosphate synthase arginine-specific large


chain OS = Saccharomyces cerevisiae GN = CPA2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





97
Q00955
58
250197


0










ACAC_YEAST Acetyl-CoA carboxylase OS = Saccharomyces cerevisiae


GN = FAS3 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IGSFGPQEDE

0.8663
0.02199
0.1144
0.6383
4.24E+05





FFNK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





98
P32598
58
35884
0.499

1










PP12_YEAST Serine/threonine-protein phosphatase PP1-2


OS = Saccharomyces cerevisiae GN = GLC7 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GSKPGQQVD
X
0.499
0.03409
0.1183
0.9862
2959





LEENEIR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





99
P02365
58
27204
0.4787

1










RS6_YEAST 40S ribosomal protein S6 OS = Saccharomyces cerevisiae


GN = RPS6A PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
KGEQELEGLT
X
0.4787
0.01467
0.0397
0.9854
2.01E+04





DTTVPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





100
P37012
57
63049


0










PGM2_YEAST Phosphoglucomutase-2 OS = Saccharomyces cerevisiae


GN = PGM2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
IIKDFPELDLG

0.6291
0.02728
0.1059
0.6921
5.18E+04





TIGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





101
P10664
57
39325
0.482
1.07
2










RL4A_YEAST 60S ribosomal protein L4-A OS = Saccharomyces cerevisiae


GN = RPL4A PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IPEIPLVVSTD
X
0.4871
0.01446
0.3459
0.9946
8.51E+05





LESIQK









2
3
IINSSEIQSAI
X
0.4381
0.02184
0.2528
0.953
9.33E+04





RPAGQATQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





102
P17536
55
23527


0










TPM1_YEAST Tropomyosin-1 OS = Saccharomyces cerevisiae GN = TPM1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
QTEQDNVEK

0.4204
0.1271
0.03615
0.4953
1.04E+04





ENQIK









2
3
NKDLEQENV

0.438
0.04989
0.1615
0.6221
6.92E+04





EKENQIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





103
P32469
55
33970


0










DPH5_YEAST Diphthine synthase OS = Saccharomyces cerevisiae


GN = DPH5 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





104
P35271
54
17115
0.5135

1










RS18_YEAST 40S ribosomal protein S18 OS = Saccharomyces cerevisiae


GN = RPS18A PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
QNDITDGKD
X
0.5135
0.01629
0.07641
0.9441
5.50E+04







YHTLANNVESK




















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





105
P13663
54
39735


0










DHAS_YEAST Aspartate-semialdehyde dehydrogenase


OS = Saccharomyces cerevisiae GN = HOM2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





106
P54839
53
54979


0










HMCS_YEAST Hydroxymethylglutaryl-CoA synthase OS = Saccharomyces


cerevisiae GN = ERG13 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DYDESLTDK

0.1337
0.1737
0.3775
0.4027
2.38E+05





NIEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





107
P40016
53
60385


0










RPN3_YEAST 26S proteasome regulatory subunit RPN3


OS = Saccharomyces cerevisiae GN = RPN3 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





108
P05317
52
33866
0.5164

1










RLA0_YEAST 60S acidic ribosomal protein P0 OS = Saccharomyces


cerevisiae GN = RPP0 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GTIEIVSDVK
X
0.5164
0.00778
0.1538
0.9872
4.30E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





109
P15992
51
23865


0










HSP26_YEAST Heat shock protein 26 OS = Saccharomyces cerevisiae


GN = HSP26 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
NQILVSGEIP

0.6438
0.03278
0.3187
0.6599
2.01E+05





STLNEESKDK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





110
P32481
50
57829


0










IF2G_YEAST Eukaryotic translation initiation factor 2 subunit gamma


OS = Saccharomyces cerevisiae GN = GCD11 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
LGDEIEIRPGI

0.6051
0.09736
0.2626
0.3614
1.13E+05





VTK









2
3
VAFTGLEEDG

0.3223
0.05784
0.09351
0.5764
1.71E+05





ETEEEKR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





111
P41056
49
12233


0










RL33B_YEAST 60S ribosomal protein L33-B OS = Saccharomyces


cerevisiae GN = RPL33B PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IEGVATPQEA

0.000032
376.9
0.3763
0.1226
1.13E+05





QFYLGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





112
P14126
49
44075


0










RL3_YEAST 60S ribosomal protein L3 OS = Saccharomyces cerevisiae


GN = RPL3 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





113
B3LLJ2
49
29059
0.5829

1










RS3A2_YEAS1 40S ribosomal protein S1-B OS = Saccharomyces


cerevisiae (strain RM11-1a) GN = RPS1B PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VSGFKDEVLE
X
0.5829
0.0184
0.1617
0.9565
4.47E+05





TV
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





114
P35997
49
8930


0










RS27A_YEAST 40S ribosomal protein S27-A OS = Saccharomyces


cerevisiae GN = RPS27A PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





115
P39954
48
49094
0.1786

1










SAHH_YEAST Adenosylhomocysteinase OS = Saccharomyces cerevisiae


GN = SAH1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
LKVPAINVND
X
0.1786
0.1265
0.1537
0.7426
1.16E+06





SVTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





116
P05736
48
27392
0.5256

1










RL2_YEAST 60S ribosomal protein L2 OS = Saccharomyces cerevisiae


GN = RPL2A PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
ASLNVGNVLP
X
0.5256
0.00852
0.3563
0.9201
1.23E+06





LGSVPEGTIV











SNVEEKPGDR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





117
Q12306
47
11662


0










SMT3_YEAST Ubiquitin-like protein SMT3 OS = Saccharomyces cerevisiae


GN = SMT3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





118
O14467
47
16394
0.7594

1










MBF1_YEAST Multiprotein-bridging factor 1 OS = Saccharomyces


cerevisiae GN = MBF1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
INEKPTVVND
X
0.7594
0.04153
0.08694
0.7815
1.61E+04





YEAAR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





119
Q08438
46
73997


0










VHS3_YEAST Protein VHS3 OS = Saccharomyces cerevisiae GN = VHS3


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





120
P38708
46
77337
0.3265

1










YHI0_YEAST Putative prolyl-tRNA synthetase YHR020W


OS = Saccharomyces cerevisiae GN = YHR020W PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IPEILEEMQG
X
0.3265
0.09196
0.1283
0.9662
6.43E+04





DLFK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





121
P40069
44
122981
0.8151

1










IMB4_YEAST Importin subunit beta-4 OS = Saccharomyces cerevisiae


GN = KAP123 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
FHEEYLPLIID
X
0.8151
0.02809
0.2967
0.9444
3.29E+04





IIDSAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





122
P05737
42
27621
0.5221

1










RL7A_YEAST 60S ribosomal protein L7-A OS = Saccharomyces cerevisiae


GN = RPL7A PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ATLELLK
X
0.5221
0.00509
0.1793
0.9871
8.87E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





123
P38715
42
37095
0.03996

1










GRE3_YEAST NADPH-dependent aldose reductase GRE3


OS = Saccharomyces cerevisiae GN = GRE3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TTPTLFENDV
X
0.03996
0.4915
0.0985
0.8748
1.48E+05





IK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





124
P15019
40
37302
0.5972

1










TAL1_YEAST Transaldolase OS = Saccharomyces cerevisiae GN = TAL1


PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
DYKGEADPG
X
0.5972
0.01513
0.05713
0.9284
1.93E+04





VISVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





125
P39939
40
13438


0










RS26B_YEAST 40S ribosomal protein S26-B OS = Saccharomyces


cerevisiae GN = RPS26B PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DLSEASVYPE

0.4244
0.02522
0.09777
0.5891
8.08E+05





YALPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





126
P25443
40
27433
0.4963

1










RS2_YEAST 40S ribosomal protein S2 OS = Saccharomyces cerevisiae


GN = RPS2 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
EFQIIDTLLPG
X
0.4963
0.00439
0.4363
0.9932
1.18E+06





LQDEVMNIKP











VQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





127
P43620
39
75867
0.5908

1










RMD8_YEAST Sporulation protein RMD8 OS = Saccharomyces cerevisiae


GN = RMD8 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
REQLLK
X
0.5908
0.00487
0.1874
0.9696
5.33E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





128
P52910
39
75765


0










ACS2_YEAST Acetyl-coenzyme A synthetase 2 OS = Saccharomyces


cerevisiae GN = ACS2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





129
P60010
38
41663


0










ACT_YEAST Actin OS = Saccharomyces cerevisiae GN = ACT1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DLTDYLMK

0.8897
0.01324
0.1224
0.6466
4.23E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





130
P41805
37
25522
0.7348

1










RL10_YEAST 60S ribosomal protein L10 OS = Saccharomyces cerevisiae


GN = RPL10 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
WGFTNLDRP
X
0.7348
0.02758
0.107
0.8056
2.97E+05





EYLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





131
Q86ZR7
37
26338


0










YKD3A_YEAST Putative uncharacterized hydrolase YKL033W-A


OS = Saccharomyces cerevisiae GN = YKL033W-A PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





132
P38205
35
77830


0










NCL1_YEAST tRNA (cytosine-5-)-methyltransferase NCL1


OS = Saccharomyces cerevisiae GN = NCL1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LSSETPALES

0.3404
0.01969
0.1416
0.3584
2.22E+04





EGPQTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





133
P17255
35
118562


0










VATA_YEAST V-type proton ATPase cataytic subunit A


OS = Saccharomyces cerevisiae GN = TFP1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
AIKEESQSIYI

0.2979
0.2188
0.09557
0.4074
1.46E+05





PR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





134
P05739
35
20183
0.5423

1










RL6B_YEAST 60S ribosomal protein L6-B OS = Saccharomyces cerevisiae


GN = RPL6B PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
HLEDNTLLVT
X
0.5423
0.02668
0.2265
0.9184
1.35E+05





GPFK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





135
Q07530
35
34457
0.9709

1










YD114_YEAST Uncharacterized oxidoreductase YDL114W


OS = Saccharomyces cerevisiae GN = YDL114W PE = 2 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
INRASGTTK
X
0.9709
0.00996
0.1262
0.9924
1.27E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





136
P15625
34
57804


0










SYFA_YEAST Phenylalanyl-tRNA synthetase alpha chain


OS = Saccharomyces cerevisiae GN = FRS2 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





137
Q02209
33
41274
0.9909

1










YKZ1_YEAST Uncharacterized protein YKR011C OS = Saccharomyces


cerevisiae GN = YKR011C PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
FQLVEK
X
0.9909
0.00329
0.1232
0.9948
5.97E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





138
A6ZZJ1
32
86
0.5908

1










MYO3_YEAS7 Myosin-3 OS = Saccharomyces cerevisiae (strain YJM789)


GN = MYO3 PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
RIDAAIK
X
0.5908
0.00487
0.1874
0.9696
5.33E+05



2
3
IIKSANELVET

0.5256
0.06512
0.2213
0.1936
2.39E+05





LSK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





139
P40077
32
64327


0










DSE1_YEAST Protein DSE1 OS = Saccharomyces cerevisiae GN = DSE1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
MNSPILRK

0.003135
3.635
0.06896
0.9784
7203
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





140
A7A1S5
31
76547


0










DUS3_YEAS7 tRNA-dihydrouridine synthase 3 OS = Saccharomyces


cerevisiae (strain YJM789) GN = DUS3 PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
QNENQK

0.4468
0.05701
0.00365
0.6454
6837
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





141
P02557
31
51011


0










TBB_YEAST Tubulin beta chain OS = Saccharomyces cerevisiae GN = TUB2


PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





142
P17423
31
38792


0










KHSE_YEAST Homoserine kinase OS = Saccharomyces cerevisiae


GN = THR1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





143
P04076
30
52173


0










ARLY_YEAST Argininosuccinate lyase OS = Saccharomyces cerevisiae


GN = ARG4 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





144
A6ZWD3
29
68204


0










DBP1_YEAS7 ATP-dependent RNA helicase DBP1 OS = Saccharomyces


cerevisiae (strain YJM789) GN = DBP1 PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





145
P07702
29
155248


0










LYS2_YEAST L-aminoadipate-semialdehyde dehydrogenase


OS = Saccharomyces cerevisiae GN = LYS2 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EYFVEPNSAE

0.0214
0.957
0.3831
0.02822
9.46E+05





GK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





146
P39976
27
55190


0










DLD3_YEAST D-lactate dehydrogenase [cytochrome] 3


OS = Saccharomyces cerevisiae GN = DLD3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
LNAAGLIGDA

1
0.00277
0.1741
0.2978
8.97E+04





PKPVVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





147
P53953
27
98881
0.4536

1










SFB2_YEAST SED5-binding protein 2 OS = Saccharomyces cerevisiae


GN = SFB2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SEQGILNTPK
X
0.4536
0.03249
0.3059
0.9489
4.80E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





148
Q08647
27
77419


0










PUS7_YEAST Multisubstrate pseudouridine synthase 7


OS = Saccharomyces cerevisiae GN = PUS7 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





149
Q07798
26
102104
0.9876

1










SPO75_YEAST Sporulation-specific protein 75 OS = Saccharomyces


cerevisiae GN = SPO75 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ILDKIIR
X
0.9876
0.00489
0.02083
0.9895
5.42E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





150
P29509
26
34409
0.3208

1










TRXB1_YEAST Thioredoxin reductase 1 OS = Saccharomyces cerevisiae


GN = TRR1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IVAGQVDTD
X
0.3208
0.06408
0.4281
0.9649
5.48E+05





EAGYIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





151
P38720
26
53774


0










6PGD1_YEAST 6-phosphogluconate dehydrogenase, decarboxyating 1


OS = Saccharomyces cerevisiae GN = GND1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





152
P26785
26
22444


0










RL16B_YEAST 60S ribosomal protein L16-B OS = Saccharomyces


cerevisiae GN = RPL16B PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





153
P06843
25
38928
0.5908

1










SPT2_YEAST Protein SPT2 OS = Saccharomyces cerevisiae GN = SPT2


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
RQELLK
X
0.5908
0.00487
0.1874
0.9696
5.33E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





154
P06101
25
58845
0.9702

1










CDC37_YEAST Hsp90 co-chaperone Cdc37 OS = Saccharomyces


cerevisiae GN = CDC37 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VFEDIPIEEAEK
X
0.9702
0.01138
0.1397
0.737
1.27E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





155
P07149
25
228547


0










FAS1_YEAST Fatty acid synthase subunit beta OS = Saccharomyces


cerevisiae GN = FAS1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
WETTTQFK

0.3417
0.07701
0.06965
0.6964
5.87E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





156
P35169
24
280962
1.001

1










TOR1_YEAST Serine/threonine-protein kinase TOR1 OS = Saccharomyces


cerevisiae GN = TOR1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EIKFIK
X
1.001
0
0.1891
0.9934
1.08E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





157
Q05016
24
29301


0










YM71_YEAST Uncharacterized oxidoreductase YMR226C


OS = Saccharomyces cerevisiae GN = YMR226C PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
IKPFIENLPQE

0.4711
0.02328
0.1926
0.2766
5.31E+04





FK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





158
P23796
24
59181


0










RIT1_YEAST tRNA A64-2′-O-ribosylphosphate transferase


OS = Saccharomyces cerevisiae GN = RIT1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LNELFMGK

0.173
0.1599
0.1023
0.6886
5.41E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





159
Q12734
23
124772
0.9979

1










CSR2_YEAST Transcription factor CSR2 OS = Saccharomyces cerevisiae


GN = CSR2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
STTLSDIK
X
0.9979
0
0.5316
0.9992
3.05E+06
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





160
P24384
23
130674
0.5908

1










PRP22_YEAST Pre-mRNA-splicing factor ATP-dependent RNA helicase


PRP22 OS = Saccharomyces cerevisiae GN = PRP22 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ERALGIK
X
0.5908
0.00487
0.1874
0.9696
5.33E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





161
Q04412
23
54780
0.9523

1










AGE1_YEAST ADP-ribosylation factor GTPase-activating protein effector


protein 1 OS = Saccharomyces cerevisiae GN = AGE1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LTNILLK
X
0.9523
0.00751
0.01207
0.9072
1.83E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





162
P53191
22
70950


0










PIB2_YEAST Phosphatidylinositol-3-phosphate-binding protein 2


OS = Saccharomyces cerevisiae GN = PIB2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





163
Q03497
22
102940
1

1










STE20_YEAST Serine/threonine-protein kinase STE20


OS = Saccharomyces cerevisiae GN = STE20 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ETLSGLEFLH
X
1
0.00609
0.6136
0.9975
1.27E+06







SK




















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





164
P40462
22
107655
0.9911

1










TM108_YEAST Protein TMA108 OS = Saccharomyces cerevisiae


GN = TMA108 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
FINLEK
X
0.9911
0.00377
0.122
0.9964
5.91E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





165
P05755
22
22285


0










RS9B_YEAST 40S ribosomal protein S9-B OS = Saccharomyces cerevisiae


GN = RPS9B PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LDYVLALK

0.005702
1.64
0.079
0.8879
9978
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





166
P46679
22
97766


0










STB2_YEAST Protein STB2 OS = Saccharomyces cerevisiae GN = STB2


PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
SSLQGQGKT

0.9544
0.00932
0.1894
0.3151
7.47E+05





GICSAIDPKS











DK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





167
P0C0W1
22
14705


0










RS22A_YEAST 40S ribosomal protein S22-A OS = Saccharomyces


cerevisiae GN = RPS22A PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





168
P36096
22
88064
0.9908

1










TUL1_YEAST Transmembrane E3 ubiquitin-protein ligase 1


OS = Saccharomyces cerevisiae GN = TUL1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IDLVSNNK
X
0.9908
0.00823
0.03719
0.9728
1.54E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





169
P38967
21
65362


0










TAT2_YEAST Tryptophan permease OS = Saccharomyces cerevisiae


GN = TAT2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





170
Q05955
21
57795
0.8578

1










ADY4_YEAST Accumulates dyads protein 4 OS = Saccharomyces


cerevisiae GN = ADY4 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DVDYQTFK
X
0.8578
0.03111
0.08023
0.9212
1.78E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





171
P26786
21
21761


0










RS7A_YEAST 40S ribosomal protein S7-A OS = Saccharomyces cerevisiae


GN = RPS7A PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





172
P18759
21
84004
1

1










SEC18_YEAST Vesicular-fusion protein SEC18 OS = Saccharomyces


cerevisiae GN = SEC18 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
FKIPGFGK
X
1
0.00372
0.3628
0.9814
2.01E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





173
P02309
21
11361
0.4287

1










H4_YEAST Histone H4 OS = Saccharomyces cerevisiae GN = HHF1 PE = 1


SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DSVTYTEHAK
X
0.4287
0.05722
0.06178
0.844
1.78E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





174
P36139
20
31428


0










PET10_YEAST Protein PET10 OS = Saccharomyces cerevisiae GN = PET10


PE = 1 SV = 3




















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LDELVNLLVFK

−0.001257
0.6587
0.7685
0.9993
1.17E+06
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





175
Q02773
20
140029


1










RPM2_YEAST Ribonuclease P protein component, mitochondrial


OS = Saccharomyces cerevisiae GN = RPM2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SLLRKSKPLQA
X
0
999
0.00047
0.8095
271.1
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





176
P38697
20
56494
0.3128

1










IMDH2_YEAST Inosine-5′-monophosphate dehydrogenase IMD2


OS = Saccharomyces cerevisiae GN = IMD2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
TASAQLEGG
X
0.3128
0.09825
0.218
0.8306
1.40E+04





VHNLHSYEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





177
P41832
20
221017
0.02392

1










BNI1_YEAST Protein BNI1 OS = Saccharomyces cerevisiae GN = BNI1


PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
RLKELETK
X
0.02392
0.2888
0.00547
0.8577
1621
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





178
P17119
20
83952
0.09389

1










KAR3_YEAST Kinesin-like protein KAR3 OS = Saccharomyces cerevisiae


GN = KAR3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TNLETLEK
X
0.09389
0.2254
0.0084
0.9135
5.14E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





179
P15303
20
85579


0










SEC23_YEAST Protein transport protein SEC23 OS = Saccharomyces


cerevisiae GN = SEC23 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





180
P32565
20
104768


0










RPN2_YEAST 26S proteasome regulatory subunit RPN2


OS = Saccharomyces cerevisiae GN = RPN2 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





181
Q03660
20
128787


0










TR130_YEAST Transport protein particle 130 kDa subunit


OS = Saccharomyces cerevisiae GN = TRS130 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





182
P39081
19
71853


0










PCF11_YEAST Protein PCF11 OS = Saccharomyces cerevisiae GN = PCF11


PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
INNLYASLKA

0.9323
0.01402
0.3541
0.6434
6.37E+04





EGLIYTPPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





183
B3LRC2
19
36810


0










UTH1_YEAS1 Protein UTH1 OS = Saccharomyces cerevisiae (strain RM11-


1a) GN = UTH1 PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





184
P07259
19
244972


0










PYR1_YEAST Protein URA1 OS = Saccharomyces cerevisiae GN = URA2


PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





185
P18963
19
350758
0.9999

1










IRA1_YEAST Inhibitory regulator protein IRA1 OS = Saccharomyces


cerevisiae GN = IRA1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GNKYLIK
X
0.9999
0.00158
0.0893
0.9713
3.78E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





186
P38850
18
123854


0










RT107_YEAST Regulator of Ty1 transposition protein 107


OS = Saccharomyces cerevisiae GN = RTT107 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





187
Q04199
18
51420


0










CAC2_YEAST Chromatin assembly factor 1 subunit p60


OS = Saccharomyces cerevisiae GN = CAC2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IPCNSSDSK

0.9943
0.00328
0.1865
0.52
1.44E+06
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





188
Q12345
17
28402


0










IES3_YEAST Ino eighty subunit 3 OS = Saccharomyces cerevisiae


GN = IES3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
IDILTKIQENL

0.04155
1.417
0.06472
0.5595
1068







LEEYQK




















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





189
P53598
17
35010
1.001

1










SUCA_YEAST Succinyl-CoA ligase [ADP-forming] subunit alpha


mitochondrial OS = Saccharomyces cerevisiae GN = LSC1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ESIPYDK
X
1.001
0.001
0.6215
0.9959
3.11E+06
















TABLE 2





Proteins identified by Mascot Distiller from ChAP-MS analysis of GAL1


chromatin isolated from cells grown in galactose.


Mascot Distiller


Quantitation Report







Mascot search results: Galactose












Log





ratio




versus
Log ratio




Intensity
versus




(all
Intensity




positive
(selected




ratios)
ratios)







L/(L + H)
0
0




2.00e+7
5.00e+6




4.00e+7
1.00e+7




6.00e+7
1.50e+7 −6




−15 −10
−4 −2 0 2




−5 0 5

















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





1
P00924
952
46773
0.727
1.077
10










ENO1_YEAST Enolase 1 OS = Saccharomyces cerevisiae GN = ENO1


PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
RIATAIEK
X
0.9922
0.001
0.0623
0.9937
78080.00


2
2
VNQIGTLS
X
0.7237
0.001
0.6107
0.9971
1.48E+06




ESIK


3
3
AVDDFLISL
X
0.6953
0.00258
0.5605
0.9825
2.57E+05




DGTANK


4
2
AVDDFLISL
X
0.678
0.00158
0.1606
0.9839
3.20E+06




DGTANK


5
2
TAGIQIVA
X
0.8499
0
0.4502
0.9983
8.74E+05




DDLTVTNPK


6
3
IEEELGDN
X
0.7139
0.01531
0.04418
0.7314
3.10E+04




AVFAGENF




HHGDK


7
2
IEEELGDN
X
0.8709
0.00321
0.8165
0.9933
1.28E+05




AVFAGENF




HHGDKL


8
3
IEEELGDN
X
0.8482
0.00579
0.7751
0.9956
5.69E+05




AVFAGENF




HHGDKL


9
3
YPIVSIEDP
X
0.743
0.001
0.7934
0.9984
1.74E+06




FAEDDWEA




WSHFFK


10
3
RYPIVSIED

0.2589
0.1734
0.2248
0.5408
1353




PFAEDDWE




AWSHFFK


11
3
YGASAGNV
X
0.7223
0.00158
0.9201
0.9993
1.05E+07




GDEGGVAP




NIQTAEEAL




DLIVDAIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





2
P00925
827
46885
0.7156
1.024
5










ENO2_YEAST Enolase 2 OS = Saccharomyces cerevisiae GN = ENO2


PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VNQIGTLS
X
0.7237
0.001
0.6107
0.9971
1.48E+06




ESIK


2
3
AVDDFLLS
X
0.6953
0.00258
0.5605
0.9825
2.57E+05




LDGTANK


3
2
AVDDFLLS
X
0.678
0.00158
0.1606
0.9839
3.20E+06




LDGTANK


4
2
DGKYDLDF

0.593
0.03836
0.2515
0.6481
3.31E+05




KNPESDK


5
3
DGKYDLDF

0.2183
0.1283
0.2233
0.1889
8.04E+05




KNPESDK


6
3
YPIVSIEDP
X
0.743
0.001
0.7934
0.9984
1.74E+06




FAEDDWEA




WSHFFK


7
3
RYPIVSIED

0.2589
0.1734
0.2248
0.5408
1353




PFAEDDWE




AWSHFFK


8
3
YGASAGNV
X
0.7223
0.00158
0.9201
0.9993
1.05E+07




GDEGGVAP




NIQTAEEAL




DLIVDAIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





3
P00359
773
35724
0.6771
1.019
7










G3P3_YEAST Glyceraldehyde-3-phosphate dehydrogenase 3


OS = Saccharomyces cerevisiae GN = TDH3 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
ETTYDEIKK
X
0.6838
0.00472
0.3538
0.9553
3.68E+05


2
2
TASGNIIPS
X
0.6648
0.00158
0.6513
0.9983
3.86E+06




STGAAK


3
2
VPTVDVSV
X
0.7282
0.0064
0.2127
0.8286
6.60E+05




VDLTVK


4
3
LNKETTYD

0.7548
0.04527
0.0313
0.2068
5.04E+04




EIKK


5
3
YAGEVSHD

0.688
0.0049
0.1652
0.6807
4.07E+06




DKHIIVDGK


6
2
YAGEVSHD
X
0.6826
0.00224
0.3878
0.8652
2.07E+06




DKHIIVDGK


7
3
KVVITAPSS
X
0.7193
0.00631
0.1023
0.9512
2.42E+05




TAPMFVMG




VNEEK


8
2
DPANLPWG
X
0.6776
0.00494
0.5179
0.9695
1.47E+06




SSNVDIAI




DSTGVFK


9
3
DPANLPWG

0.6946
0.02605
0.3559
0.4268
1.47E+06




SSNVDIAI




DSTGVFK


10
3
VINDAFGIE
X
0.6612
0.0114
0.3918
0.9512
5.69E+05




EGLMTTVH




SLTATQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





4
P02994
662
50394
0.8504
1.012
7










EF1A_YEAST Elongation factor 1-alpha OS = Saccharomyces cerevisiae


GN = TEF1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
FDELLEK
X
0.826
0.00158
0.3074
0.9923
4.71E+06


2
3
SHINVVVI

0.8651
0.00919
0.1342
0.4249
1.91E+05




GHVDSGK


3
2
TLLEAIDAI
X
0.8558
0
0.7243
0.9974
1.11E+06




EQPSRPTD




KPLR


4
3
TLLEAIDAI
X
0.8371
0.00322
0.6393
0.9893
8.82E+06




EQPSRPTD




KPLR


5
3
VETGVIKP
X
0.8774
0.001
0.7139
0.9992
6.53E+06




GMVVTFAP




AGVTTEVK


6
2
VETGVIKP
X
0.8911
0
0.7784
0.9982
2.27E+06




GMVVTFAP




AGVTTEVK


7
3
SVEMHHEQ
X
0.8474
0.00071
0.7764
0.9988
1.10E+07




LEQGVPGD




NVGFNVK


8
2
SVEMHHEQ
X
0.8482
0.001
0.8709
0.999
1.09E+06




LEQGVPGD




NVGFNVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





5
P54115
486
54380
0.6881
1.024
5










ALDH6_YEAST Magnesium-activated aldehyde dehydrogenase,


cytosolic OS = Saccharomyces cerevisiae GN = ALD6 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SVAVDSSE
X
0.7081
0.0109
0.05156
0.971
5.45E+05




SNLK


2
3
SVAVDSSE
X
0.6272
0.01694
0.1014
0.9286
2.04E+05




SNLKK


3
2
SVAVDSSE
X
0.6886
0.00158
0.2331
0.997
7.45E+05




SNLKK


4
3
SAHLVFDD
X
0.6792
0.004
0.1402
0.9596
2.03E+05




ANIKK


5
3
IVKEEIFGP

0.2547
0.07849
0.4923
0.06903
3.53E+06




VVTVAK


6
2
IVKEEIFGP
X
0.6996
0.00158
0.1833
0.9947
3.23E+05




VVTVAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





6
P10591
482
70039
0.8188
1.018
4










HSP71_YEAST Heat shock protein SSA1 OS = Saccharomyces


cerevisiae GN = SSA1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
MKETAESY
X
0.7735
0.00986
0.2692
0.9866
2.32E+05




LGAK


2
2
NFNDPEVQ
X
0.8218
0.00856
0.2133
0.9657
9.80E+05




ADMK


3
2
NQAAMNPS
X
0.8186
0.0035
0.4594
0.9975
1.37E+06




NTVFDAK


4
3
NTISEAGD

0.3583
0.06491
0.4424
0.4808
1.01E+07




KLEQADKD




TVTK


5
2
NTISEAGD
X
0.8301
0.00158
0.6157
0.995
7.24E+05




KLEQADKD




TVTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





7
P50095
425
56813
0.9382
1.024
5










IMDH3_YEAST Probable inosine-5′-monophosphate dehydrogenase


IMD3 OS = Saccharomyces cerevisiae GN = IMD3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
TASAQLEG

0.4222
0.1268
0.5294
0.3116
7.78E+05




GVHNLHSY




EK


2
2
TASAQLEG
X
0.893
0.02366
0.2283
0.9113
2.44E+05




GVHNLHSY




EK


3
2
NPVTGAQG
X
0.9433
0.00754
0.3647
0.9924
1.01E+06




ITLSEGNEI




LK


4
3
NPVTGAQG
X
0.9335
0.00158
0.3228
0.9933
3.39E+05




ITLSEGNEI




LK


5
2
YFSESDSV
X
1
0.001
0.4121
0.9864
7.24E+04




LVAQGVSG




AVVDK


6
2
GGLTYNDF
X
0.9534
0
0.8179
0.9932
2.35E+05




LVLPGLVDF




PSSEVSLQ




TK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





8
P07262
383
49539
0.5666
1.061
3










DHE4_YEAST NADP-specific glutamate dehydrogenase 1


OS = Saccharomyces cerevisiae GN = GDH1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
STATGPSE
X
0.6132
0.00959
0.3565
0.9733
2.44E+05




AVWYGPPK


2
3
VTWENDK
X
0.535
0.02836
0.5322
0.8087
5.75E+05




GEQEVAQG




YR


3
2
VTWENDK
X
0.6306
0.00328
0.4773
0.9937
1.29E+05




GEQEVAQG




YR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





9
P06169
369
61737
0.5627

5










PDC1_YEAST Pyruvate decarboxylase isozyme 1 OS = Saccharomyces


cerevisiae GN = PDC1 PE = 1 SV = 7

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VATTGEWD
X
0.5604
0.00308
0.3782
0.9946
8.35E+05




KLTQDK


2
3
YGGVYVGT
X
0.5512
0.00325
0.3138
0.9816
4.29E+05




LSKPEVK


3
2
YGGVYVGT
X
0.5578
0.001
0.3925
0.9961
8.00E+05




LSKPEVK


4
3
LLQTPIDM
X
0.6389
0.08423
0.3737
0.9119
2000




SLKPNDAE




SEK


5
2
MIEIMLPVF
X
0.6331
0.00453
0.5965
0.979
1.63E+05




DAPQNLVE




QAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





10
P29311
363
30209
0.7744
1.108
3










BMH1_YEAST Protein BMH1 OS = Saccharomyces cerevisiae GN = BMH1


PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
QAFDDAIA
X
0.7998
0.00255
0.5395
0.9946
4.35E+05




ELDTLSEES




YK


2
2
ISDDILSVL
X
0.625
0.01278
0.271
0.7283
1.76E+05




DSHLIPSAT




TGESK


3
3
ISDDILSVL
X
0.7868
0.00158
0.1746
0.9972
1.49E+06




DSHLIPSAT




TGESK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





11
P15108
361
81435
0.007455

6










HSC82_YEAST ATP-dependent molecular chaperone HSC82


OS = Saccharomyces cerevisiae GN = HSC82 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
AILFIPK
X
0.7304
0.00664
0.3427
0.9954
5.12E+04


2
2
RVDEGGA
X
0.734
0.007
0.04224
0.965
9084




QDK


3
2
KDEDDKKPK

0.4443
0.1702
0.04474
0.339
2202


4
2
ALKDILGD
X
0.7398
0.01231
0.03927
0.8976
8.40E+04




QVEK


5
3
VKEEVQEL
X
0.711
0.00306
0.1697
0.9942
2.85E+05




EELNK


6
2
LEEVDEEE
X
0.6241
0.03842
0.06528
0.873
2.25E+05




EEKKPK


7
3
TLVDITKDF
X
0.005607
0.09361
0.4759
0.9104
1.04E+07




ELEETDEEK




AER
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





12
P46655
353
81369
0.8084

4










SYEC_YEAST Glutamyl-tRNA synthetase, cytoplasmic


OS = Saccharomyces cerevisiae GN = GUS1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ANFEIDLPD
X
0.8028
0.00578
0.1682
0.9743
6.26E+05




AK


2
2
IHLEGSEAP
X
0.8001
0.01046
0.2506
0.9636
5.39E+05




QEPK


3
3
EKEEFQDS
X
0.8258
0.00576
0.2679
0.9657
5.87E+05




ILEDLDLLG




IK


4
2
EKEEFQDS
X
0.7985
0.00441
0.3707
0.9948
1.96E+05




ILEDLDLLG




IK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





13
P32589
346
77318
0.7318
1.014
3










HSP7F_YEAST Heat shock protein homolog SSE1 OS = Saccharomyces


cerevisiae GN = SSE1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EELEELVKP
X
0.7536
0.03052
0.07918
0.8999
7.17E+04




LLER


2
2
GKLEEEYA

0.6193
0.01623
0.1684
0.5929
1.11E+06




PFASDAEK


3
2
IIGLDYHHP
X
0.7328
0.01091
0.08547
0.9763
8.03E+04




DFEQESK


4
3
QVEDEDH
X
0.7218
0.01002
0.3701
0.8889
1.59E+05




MEVFPAGS




SFPSTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





14
P00560
322
44711
0.5639
1.448
3










PGK_YEAST Phosphoglycerate kinase OS = Saccharomyces cerevisiae


GN = PGK1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VDFNVPLD
X
0.272
0.04331
0.3024
0.8665
1.97E+06




GK


2
2
VLENTEIG

0.9987
0
0.8558
0.2984
5.35E+07




DSIFDK


3
2
SSAAGNTV
X
0.7606
0.00838
0.6009
0.9775
2.98E+06




IIGGGDTA




TVAK


4
2
GVEVVLPV
X
0.8169
0.00271
0.6174
0.9986
1.47E+06




DFIIADAFS




ADANTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





15
P00549
296
54807
0.7976
1.025
5










KPYK1_YEAST Pyruvate kinase 1 OS = Saccharomyces cerevisiae


GN = PYK1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
MNFSHGSY
X
0.7461
0.02847
0.1614
0.8404
2.71E+05




EYHK


2
2
MNFSHGSY
X
0.8117
0.00999
0.1068
0.9731
4.19E+05




EYHK


3
2
GVNLPGTD
X
0.8043
0.00272
0.5459
0.9882
6.30E+06




VDLPALSEK


4
2
GDLGIEIPA
X
0.7994
0.001
0.5602
0.9987
7.61E+06




PEVLAVQK


5
2
SEELYPGRP

0.002097
3.304
0.1291
0.6758
1.89E+05




LAIALDTK


6
3
KSEELYPG
X
0.7575
0.00877
0.1331
0.7972
1.12E+06




RPLAIALDTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





16
P38720
295
53509
0.9328
1.029
4










6PGD1_YEAST 6-phosphogluconate dehydrogenase, decarboxylating 1


OS = Saccharomyces cerevisiae GN = GND1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SIIGATSIE
X
0.9129
0.001
0.1873
0.9973
1.68E+05




DFISK


2
3
LGGFTDKE
X
0.949
0.00158
0.2086
0.9846
6.26E+05




ISDVFAK


3
2
AYREEPDL
X
0.936
0.00484
0.3345
0.723
3.06E+06




ENLLFNK


4
3
YGPSLMPG
X
0.8712
0.00561
0.3785
0.9595
2.62E+05




GSEEAWPH




IK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





17
P04385
290
57907
0.6139
1.13
4










GAL1_YEAST Galactokinase OS = Saccharomyces cerevisiae GN = GAL1


PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
NPSITLINA
X
0.7365
0.001
0.5381
0.9953
2.36E+06




DPK


2
3
MLVLVEES
X
0.7882
0.0105
0.2982
0.9203
2.53E+05




LANKK


3
2
SHSEEVIVP
X
0.5377
0.04126
0.3609
0.9033
3.79E+06




EFNSSAK


4
2
VLNEKNPSI
X
0.7577
0.00342
0.1352
0.9951
4.28E+04




TLINADPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





18
P04397
264
78146
0.6778

7










GAL10_YEAST Bifunctional protein GAL10 OS = Saccharomyces


cerevisiae GN = GAL10 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
1
LEVLTK
X
0.8734
0.001
0.01287
0.9936
9.32E+04


2
2
DYIHVVDL
X
0.8614
0.00158
0.2342
0.9952
1.38E+06




AK


3
3
DYIHVVDL
X
0.9574
0
0.4691
0.9578
4.66E+05




AK


4
2
AGDVLNLT
X
0.8088
0.00531
0.07739
0.9941
4.67E+05




AKPDR


5
2
EIATFNSTK
X
1.003
0.01104
0.02312
0.9843
1.39E+04




PTVLGPK


6
2
YAIENILND
X
0.5331
0.02963
0.3656
0.7372
2.83E+06




LYNSDK


7
2
SVDVDKN
X
0.8696
0.00158
0.2804
0.9956
3.03E+05




MIPTGNIV




DR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





19
P11484
262
66561
0.8176
1.003
3










HSP75_YEAST Heat shock protein SSB1 OS = Saccharomyces


cerevisiae GN = SSB1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LLSDFFDGK
X
0.8188
0.001
0.534
0.998
9.62E+05


2
2
RFDDESVQK
X
0.8212
0.00341
0.3458
0.9841
1.10E+06


3
2
ENTLLGEF
X
0.8144
0.00158
0.4074
0.9981
1.59E+06




DLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





20
P08431
261
42358
0.6343
8.653
3










GAL7_YEAST Galactose-1-phosphate uridylyltransferase


OS = Saccharomyces cerevisiae GN = GAL7 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
EHNTDLFA
X
0.01158
0.4988
0.2836
0.9602
5.87E+05




DYVK


2
2
LDQPILPQ
X
0.918
0
0.8548
0.9997
6.17E+06




NDSNEDNLK


3
3
RPWLGQQ
X
0.7836
0.01208
0.1133
0.9209
3.76E+05




EAAYKPTA




PLYDPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





21
Q01560
247
45444


0










NOP3_YEAST Nucleolar protein 3 OS = Saccharomyces cerevisiae


GN = NPL3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





22
P07284
238
53677
0.2383

4










SYSC_YEAST Seryl-tRNA synthetase, cytoplasmic OS = Saccharomyces


cerevisiae GN = SES1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
YIPGEPEFL
X
0.8227
0.00158
0.4653
0.9473
1.11E+05




PFVNELPK


2
3
NASVEIVD
X
0.7951
0.00573
0.4831
0.9887
3.44E+05




EIISDYKD




WVK


3
2
NASVEIVD
X
0.7696
0.01392
0.1984
0.9426
6.67E+04




EIISDYKD




WVK


4
3
IEQFVITEP
X
0.114
0.1522
0.1374
0.9075
8.56E+05




EKSWEEFEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





23
P38088
234
75364
0.8224
1.006
2










SYG_YEAST Glycyl-tRNA synthetase 1 OS = Saccharomyces cerevisiae


GN = GRS1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IDDSGVSI
X
0.8259
0.01171
0.1781
0.9752
4.43E+05




GK


2
2
LDDDVVKE
X
0.8161
0.01051
0.07847
0.9658
2.44E+05




YEEILAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





24
P17709
225
55342
0.1024
15.72
2










HXKG_YEAST Glucokinase-1 OS = Saccharomyces cerevisiae GN = GLK1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EGHTLASDK
X
0.003844
0.1695
0.7656
0.9015
6.01E+05


2
2
YDVVIDQK
X
0.836
0.0107
0.2711
0.9649
9.39E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





25
P10592
223
69844
0.6324
1.099
3










HSP72_YEAST Heat shock protein SSA2 OS = Saccharomyces


cerevisiae GN = SSA2 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
MKETAESY
X
0.7735
0.00986
0.2692
0.9866
2.32E+05




LGAK


2
2
NFNDPEVQ
X
0.5921
0.01773
0.3417
0.9151
3.96E+05




GDMK


3
3
NTISEAGD
X
0.6179
0.00324
0.3113
0.9818
8.87E+05




KLEQADKD




AVTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





26
P34760
203
21688
0.8525

1










TSA1_YEAST Peroxiredoxin TSA1 OS = Saccharomyces cerevisiae


GN = TSA1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TAVVDGVF
X
0.8525
0.003
0.2304
0.9765
1.37E+06




DEVSLDK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





27
P07806
202
126596
0.902
1.08
2










SYV_YEAST Valyl-tRNA synthetase, mitochondrial OS = Saccharomyces


cerevisiae GN = VAS1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TAEDQKDS
X
0.8245
0.0142
0.06813
0.9834
6.02E+04




IVSLIK


2
2
TGEVIINPL
X
0.9585
0.02748
0.09926
0.894
8.93E+04




KEDGSPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





28
P39015
200
29977
0.8734
1.037
2










STM1_YEAST Suppressor protein STM1 OS = Saccharomyces cerevisiae


GN = STM1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
TAQLSLQD
X
0.9037
0.0159
0.345
0.8549
1.14E+05




YLNQQANN




QFNK


2
2
EAQADAAA
X
0.8405
0.03245
0.2666
0.956
1.01E+05




EIAEDAAE




AEDAGKPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





29
P14540
196
39596
0.7378
1.02
2










ALF_YEAST Fructose-bisphosphate aldolase OS = Saccharomyces


cerevisiae GN = FBA1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GISNEGQN
X
0.7232
0.00563
0.2971
0.9957
2.70E+06




ASIK


2
2
LLPWFDGM
X
0.7527
0.00701
0.6657
0.9971
2.69E+06




LEADEAYFK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





30
P07259
183
245990
0.6064

1










PYR1_YEAST Protein URA1 OS = Saccharomyces cerevisiae GN = URA2


PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SISGPVITD
X
0.6064
0.03681
0.07372
0.792
2.43E+05




VASLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





31
P16521
177
115920
0.7059
1.311
3










EF3A_YEAST Elongation factor 3A OS = Saccharomyces cerevisiae


GN = YEF3 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TQLRLKR
X
0.9013
0.00444
0.3845
0.99
2.38E+06


2
2
AYEELSNT
X
0.7997
0.02628
0.5649
0.9771
1.97E+06




DLEFK


3
3
AYEELSNT
X
0.3863
0.03175
0.257
0.8484
1.37E+06




DLEFKFPEP




GYLEGVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





32
P11412
168
57830
0.5867
1.242
2










G6PD_YEAST Glucose-6-phosphate 1-dehydrogenase


OS = Saccharomyces cerevisiae GN = ZWF1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
AVAPIDTD
X
0.5629
0.04227
0.2849
0.9375
7.08E+05




DVLLGQYGK


2
3
SEDGSKPA
X
0.7949
0.00856
0.1299
0.9748
9.45E+04




YVDDDTVD




KDSK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





33
P07149
160
228547
0.8094

1










FAS1_YEAST Fatty acid synthase subunit beta OS = Saccharomyces


cerevisiae GN = FAS1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GNYTDFEN
X
0.8094
0.01799
0.0845
0.9521
3.39E+05




TFQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





34
P28240
159
62369
0.3227

1










ACEA_YEAST Isocitrate lyase OS = Saccharomyces cerevisiae GN = ICL1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LDADAAEI
X
0.3227
0.07711
0.202
0.9617
8.83E+05




EK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





35
P00330
155
36800
0.8664
1.009
3










ADH1_YEAST Alcohol dehydrogenase 1 OS = Saccharomyces cerevisiae


GN = ADH1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VVGLSTLPE
X
0.8678
0.00158
0.5758
0.9962
2.12E+06




IYEK


2
2
VLGIDGGE
X
0.8513
0.00158
0.397
0.9977
2.05E+06




GKEELFR


3
3
VLGIDGGE
X
0.8778
0.00344
0.5496
0.9935
2.51E+06




GKEELFR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





36
P32527
155
48990
0.8655

1










ZUO1_YEAST Zuotin OS = Saccharomyces cerevisiae GN = ZUO1 PE = 1


SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
ATTIDEQV
X
0.8655
0.00448
0.4525
0.9613
2.75E+05




GLIVDSLN




DEELVSTA




DK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





37
P04806
155
53705
0.8304

1










HXKA_YEAST Hexokinase-1 OS = Saccharomyces cerevisiae GN = HXK1


PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LSGNHTFD

0.1191
0.209
0.1488
0.6634
3.26E+05




TTQSK


2
3
TKYDVAVD
X
0.8304
0.01169
0.1392
0.9589
2.37E+04




EQSPRPGQ




QAFEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





38
P05750
153
26486
0.7359

1










RS3_YEAST 40S ribosomal protein S3 OS = Saccharomyces cerevisiae


GN = RPS3 PE = 1 SV = 5

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
ALPDAVTII
X
0.7359
0.01251
0.06703
0.9895
3.55E+05




EPKEEEPIL




APSVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





39
P53252
152
38486
0.8196

1










PIL1_YEAST Sphingolipid long chain base-responsive protein PIL1


OS = Saccharomyces cerevisiae GN = PIL1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
APTASQLQ
X
0.8196
0.01915
0.2011
0.9301
1.74E+05




NPPPPPSTTK


2
3
ALLELLDDS

0.6536
0.03193
0.2367
0.6395
5.49E+05




PVTPGETR




PAYDGYEA




SK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





40
P00817
151
32280
0.467

4










IPYR_YEAST Inorganic pyrophosphatase OS = Saccharomyces


cerevisiae GN = IPP1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LNDIEDVEK
X
0.3227
0.07711
0.202
0.9617
8.83E+05


2
3
LEITKEETL
X
0.736
0.01106
0.2893
0.9314
4.97E+05




NPIIQDTK


3
3
AVGDNDPI
X
0.7062
0.00365
0.6552
0.992
1.59E+05




DVLEIGETI




AYTGQVK


4
2
AVGDNDPI
X
0.741
0.002
0.7827
0.9921
7.42E+04




DVLEIGETI




AYTGQVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





41
Q03048
144
15891


0










COFI_YEAST Cofilin OS = Saccharomyces cerevisiae GN = COF1 PE = 1


SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SGVAVADE

0.519
0.05769
0.1215
0.5982
3.04E+05




SLTAFNDLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





42
P32324
142
93230
0.7058

3










EF2_YEAST Elongation factor 2 OS = Saccharomyces cerevisiae


GN = EFT1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
WTNKDTD
X
0.7908
0.00868
0.07043
0.8558
2.83E+05




AEGKPLER


2
2
WTNKDTD
X
0.1675
0.2545
0.2121
0.7622
2.57E+05




AEGKPLER


3
3
GQVVSEEQ
X
0.8025
0.001
0.5728
0.9927
2.98E+06




RPGTPLFTVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





43
A6ZP47
141
65697


0










DED1_YEAS7 ATP-dependent RNA helicase DED1 OS = Saccharomyces


cerevisiae (strain YJM789) GN = DED1 PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DVPEPITEF

−0.00021
5.488
0.7663
0.08765
2.92E+06




TSPPLDGLL




LENIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





44
P22515
139
114195
0.756

1










UBA1_YEAST Ubiquitin-activating enzyme E1 1 OS = Saccharomyces


cerevisiae GN = UBA1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SDDSNSKP
X
0.756
0.02454
0.07431
0.9725
4.83E+04




NVDEYK


2
2
QFMYFDSL

0.000528
7.296
0.0675
0.6501
1.43E+06




ESLPDPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





45
P38701
137
14011
0.6173

1










RS20_YEAST 40S ribosomal protein S20 OS = Saccharomyces


cerevisiae GN = RPS20 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EKVEEQEQ
X
0.6173
0.00734
0.2134
0.9546
6.58E+05




QQQQIIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





46
P14742
133
80357


0










GFA1_YEAST Glucosamine--fructose-6-phosphate aminotransferase


[isomerizing] OS = Saccharomyces cerevisiae GN = GFA1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





47
P22768
133
47175


0










ASSY_YEAST Argininosuccinate synthase OS = Saccharomyces


cerevisiae GN = ARG1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





48
P10664
131
39325
0.7018
1.054
3










RL4A_YEAST 60S ribosomal protein L4-A OS = Saccharomyces


cerevisiae GN = RPL4A PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
IPEIPLVVS
X
0.7524
0.00693
0.3528
0.9385
3.17E+05




TDLESIQK


2
2
IPEIPLVVS
X
0.6885
0.00408
0.4963
0.9979
7.46E+05




TDLESIQK


3
3
IINSSEIQS
X
0.6478
0.00324
0.4073
0.9947
9.65E+04




AIRPAGQA




TQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





49
P35691
128
18849
0.8547

1










TCTP_YEAST Translationally-controlled tumor protein homolog


OS = Saccharomyces cerevisiae GN = TMA19 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DIFSNDELL
X
0.8547
0.00941
0.2439
0.9901
9.80E+05




SDAYDAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





50
P15303
127
85331


0










SEC23_YEAST Protein transport protein SEC23 OS = Saccharomyces


cerevisiae GN = SEC23 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
FFLPLEQVE

0.7553
0.01157
0.2147
0.5191
1.45E+05




FK


2
2
KAGYQDDP

0.9927
0.02465
0.1877
0.3964
5.07E+04




QYADFK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





51
Q03690
124
145076
0.5813

1










TIF31_YEAST Protein TIF31 OS = Saccharomyces cerevisiae GN = TIF31


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DANTGEEV
X
0.5813
0.0468
0.1058
0.8113
3.64E+05




TEDFVNDI




NVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





52
P04807
117
54189
0.7785
1.004
2










HXKB_YEAST Hexokinase-2 OS = Saccharomyces cerevisiae GN = HXK2


PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ELMQQIEN
X
0.7802
0.01438
0.2465
0.9009
7.27E+05




FEK


2
3
GFDIPNIEN
X
0.7742
0.01687
0.1579
0.835
2.97E+05




HDVVPMLQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





53
P43545
115
31998
0.06161

1










SNZ3_YEAST Probable pyridoxine biosynthesis protein SNZ3


OS = Saccharomyces cerevisiae GN = SNZ3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TKGEAGTG
X
0.06161
0.5232
0.2013
0.789
4.12E+05




DVSEAVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





54
P17536
115
23527
0.3192

1










TPM1_YEAST Tropomyosin-1 OS = Saccharomyces cerevisiae GN = TPM1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
KNQQLEED
X
0.3192
0.1604
0.08858
0.7363
1.43E+04




LEESDTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





55
P07264
112
85741


0










LEUC_YEAST 3-isopropylmalate dehydratase OS = Saccharomyces


cerevisiae GN = LEU1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EFEYKDQD

0.302
0.09083
0.02215
0.6239
1.86E+05




QSSPK


2
3
DDQGKDQ

0.5589
0.01861
0.2447
0.6753
2.83E+06




ETDFVLNV




EPWR


3
2
DDQGKDQ

0.8426
0.002
0.7265
0.4088
5.60E+05




ETDFVLNV




EPWR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





56
P05744
110
12219
0.6213

1










RL33A_YEAST 60S ribosomal protein L33-A OS = Saccharomyces


cerevisiae GN = RPL33A PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IEGVATPQ
X
0.6213
0.0083
0.1734
0.995
1.38E+05




DAQFYLGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





57
P36008
110
46491
0.8109

1










EF1G2_YEAST Elongation factor 1-gamma 2 OS = Saccharomyces


cerevisiae GN = TEF4 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GQDFAPAF
X
0.8109
0.01799
0.3455
0.9756
2.24E+05




DVAPDWE




SYEYTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





58
P16862
108
104953
0.8294
1.029
2










K6PF2_YEAST 6-phosphofructokinase subunit beta


OS = Saccharomyces cerevisiae GN = PFK2 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SSPDENST
X
0.8127
0.01294
0.187
0.9353
1.95E+05




LLSNDSISLK


2
3
AAEENFNA
X
0.8594
0.01841
0.2622
0.9073
1.12E+05




DDKTISDT




AAVVGVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





59
P11154
107
130539
0.9707

1










PYC1_YEAST Pyruvate carboxylase 1 OS = Saccharomyces cerevisiae


GN = PYC1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SFLSPLETD
X
0.9707
0.00158
0.4859
0.886
1.52E+06




EEIEVVIEQ




GK


2
3
EVFVSDGE

0.5025
0.07115
0.1391
0.5886
1.13E+05




NVDSSDLL




VLLEDQVP




VETK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





60
P52910
106
75765


0










ACS2_YEAST Acetyl-coenzyme A synthetase 2 OS = Saccharomyces


cerevisiae GN = ACS2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TGTEGIPMK

0.6962
0.01855
0.4457
0.1173
7.72E+06
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





61
P35844
106
49461
0.7224

1










KES1_YEAST Protein KES1 OS = Saccharomyces cerevisiae GN = KES1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
NAPSGTLV
X
0.7224
0.06623
0.06821
0.8339
1.10E+05




GDKEDR


2
3
DFDYSVTP

0.6484
0.09516
0.283
0.6012
1.42E+05




EEGALVPE




KDDTFLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





62
P36010
105
17268


0










NDK_YEAST Nucleoside diphosphate kinase OS = Saccharomyces


cerevisiae GN = YNK1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TFIAVKPD

0.03719
0.7149
0.1927
0.2162
1.95E+05




GVQR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





63
P04802
104
63861
0.8286

1










SYDC_YEAST Aspartyl-tRNA synthetase, cytoplasmic


OS = Saccharomyces cerevisiae GN = DPS1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EIGDFEDL
X
0.8286
0.00835
0.2225
0.9736
4.26E+05




STENEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





64
P12709
104
61582
0.7709
1.002
2










G6PI_YEAST Glucose-6-phosphate isomerase OS = Saccharomyces


cerevisiae GN = PGI1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
ANKPMYVD
X
0.7705
0.01145
0.2097
0.7988
5.44E+05




GVNVAPEV




DSVLK


2
2
ANKPMYVD
X
0.7726
0.02338
0.1041
0.9243
1.51E+05




GVNVAPEV




DSVLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





65
P15019
104
37302
0.8418
1.446
2










TAL1_YEAST Transaldolase OS = Saccharomyces cerevisiae GN = TAL1


PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DYKGEADP
X
0.9932
0.01166
0.08304
0.9874
3.01E+05




GVISVK


2
2
NLAGVDYL
X
0.5131
0.1041
0.121
0.9331
6.69E+04




TISPALLDK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





66
P14120
103
11504
0.6528

1










RL30_YEAST 60S ribosomal protein L30 OS = Saccharomyces


cerevisiae GN = RPL30 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VYYFQGGN
X
0.6528
0.01167
0.1559
0.9767
1.26E+05




NELGTAVGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





67
P22943
102
11806


0










HSP12_YEAST 12 kDa heat shock protein OS = Saccharomyces


cerevisiae GN = HSP12 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





68
P0C217
101
199542
0.8624
1.013
2










YL14B_YEAST Transposon Ty1-LR4 Gag-Pol polyprotein


OS = Saccharomyces cerevisiae GN = TY1B-LR4 PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DILSVDYT
X
0.8498
0.02246
0.04882
0.8124
1.27E+05




DIMK


2
2
EVHTNQDP
X
0.8722
0.01118
0.2043
0.9837
1.65E+05




LDVSASK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





69
P0C215
101
198422
0.8624
1.013
2










YL12B_YEAST Transposon Ty1-LR2 Gag-Pol polyprotein


OS = Saccharomyces cerevisiae GN = TY1B-LR2 PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DILSVDYT
X
0.8498
0.02246
0.04882
0.8124
1.27E+05




DIMK


2
2
EVHTNQDP
X
0.8722
0.01118
0.2043
0.9837
1.65E+05




LDVSASK
















Hit
Accession
Score
Mass
L(L + H)
SD(geo)
#





70
P32598
101
35884
0.8363

1










PP12_YEAST Serine/threonine-protein phosphatase PP1-2


OS = Saccharomyces cerevisiae GN = GLC7 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GSKPGQQV
X
0.8363
0.01279
0.1472
0.9874
4.79E+04




DLEENEIR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





71
P25087
99
43403
0.8036

1










ERG6_YEAST Sterol 24-C-methyltransferase OS = Saccharomyces


cerevisiae GN = ERG6 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
KPENAETP
X
0.8036
0.04785
0.08929
0.8981
4.04E+04




SQTSQEATQ
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





72
P08524
98
40458


0










FPPS_YEAST Farnesyl pyrophosphate synthase OS = Saccharomyces


cerevisiae GN = FPP1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IEQLYHEYE

0.3329
0.09842
0.4172
0.2092
1.03E+06




ESIAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





73
P15705
97
66224


0










STI1_YEAST Heat shock protein STI1 OS = Saccharomyces cerevisiae


GN = STI1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





74
P25694
97
92331
0.8407

1










CDC48_YEAST Cell division control protein 48 OS = Saccharomyces


cerevisiae GN = CDC48 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
NAPAIIFID
X
0.8407
0.0034
0.1098
0.9968
8.16E+04




EIDSIAPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





75
P00942
96
26947
0.9321

1










TPIS_YEAST Triosephosphate isomerase OS = Saccharomyces


cerevisiae GN = TPI1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ASGAFTGE
X
0.9321
0.00579
0.6559
0.9989
1.71E+06




NSVDQIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





76
P02400
95
11099


0










RLA4_YEAST 60S acidic ribosomal protein P2-beta


OS = Saccharomyces cerevisiae GN = RPP2B PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





77
P40069
94
122525


0










IMB4_YEAST Importin subunit beta-4 OS = Saccharomyces cerevisiae


GN = KAP123 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





78
P32481
93
57829
0.8691
1.017
2










IF2G_YEAST Eukaryotic translation initiation factor 2 subunit gamma


OS = Saccharomyces cerevisiae GN = GCD11 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
LGDEIEIRP

0.9246
0.04186
0.2121
0.3448
9.63E+04




GIVTK


2
3
VAFTGLEE
X
0.888
0.00751
0.1402
0.8705
2.90E+05




DGETEEEKR


3
2
EFEEGGGL
X
0.8595
0.00652
0.4126
0.9885
5.61E+05




PEQPLNPD




FSK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





79
Q12230
92
38048
0.8619

1










LSP1_YEAST Sphingolipid long chain base-responsive protein LSP1


OS = Saccharomyces cerevisiae GN = LSP1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
APTAAELQ
X
0.8619
0.03102
0.1585
0.8149
4.28E+04




APPPPPSSTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





80
P0C0W9
90
19707


0










RL11A_YEAST 60S ribosomal protein L11-A OS = Saccharomyces


cerevisiae GN = RPL11A PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VLEQLSGQ

0.007131
0.04219
0.7402
0.3062
5.33E+06




TPVQSK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





81
P38788
86
58515


0










SSZ1_YEAST Ribosome-associated complex subunit SSZ1


OS = Saccharomyces cerevisiae GN = SSZ1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





82
P41811
85
99383


0










COPB2_YEAST Coatomer subunit beta′ OS = Saccharomyces cerevisiae


GN = SEC27 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GEIEEAIEN

0.473
0.09943
0.113
0.5911
1.71E+05




VLPNVEGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





83
P38707
85
62168


0










SYNC_YEAST Asparaginyl-tRNA synthetase, cytoplasmic


OS = Saccharomyces cerevisiae GN = DED81 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SVQYVLED

0.5764
0.02059
0.2109
0.4796
4.80E+05




PIAGPLVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





84
P00899
85
56732


0










TRPE_YEAST Anthranilate synthase component 1 OS = Saccharomyces


cerevisiae GN = TRP2 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ESFLLESAK

0.9519
0.00995
0.2493
0.2379
2.91E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





85
P0C2H6
83
15522
0.6874

1










RL27A_YEAST 60S ribosomal protein L27-A OS = Saccharomyces


cerevisiae GN = RPL27A PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
NQWFFSK

0.618
0.04071
0.1012
0.5142
1.00E+05


2
2
YTLDVEAFK
X
0.6874
0.04111
0.01567
0.7996
2.90E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





86
P26321
83
33890


0










RL5_YEAST 60S ribosomal protein L5 OS = Saccharomyces cerevisiae


GN = RPL5 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





87
P38115
83
38859
0.118

1










ARA1_YEAST D-arabinose dehydrogenase [NAD(P)+] heavy chain


OS = Saccharomyces cerevisiae GN = ARA1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TMYAADGD
X
0.118
0.1798
0.2653
0.8455
1.50E+05




YLETYK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





88
P32599
82
72057


0










FIMB_YEAST Fimbrin OS = Saccharomyces cerevisiae GN = SAC6 PE = 1


SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





89
A6ZXP4
81
50248
0.3547

1










SUB2_YEAS7 ATP-dependent RNA helicase SUB2 OS = Saccharomyces


cerevisiae (strain YJM789) GN = SUB2 PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
FLQNPLEIF
X
0.3547
0.08683
0.2049
0.8314
2.82E+04




VDDEAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





90
P28273
80
140340


0










YKV5_YEAST Uncharacterized protein YKL215C OS = Saccharomyces


cerevisiae GN = YKL215C PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





91
P15625
80
57804
0.7091

1










SYFA_YEAST Phenylalanyl-tRNA synthetase alpha chain OS = accharomyces cerevisiae


GN = FRS2


PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
DLQDTFYI
X
0.7091
0.04609
0.1531
0.7641
1.01E+05




KDPLTADL




PDDK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





92
P38934
80
54606
0.2713

1










BFR1_YEAST Nuclear segregation protein BFR1 OS = Saccharomyces


cerevisiae GN = BFR1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
INEIEESIA
X
0.2713
0.04844
0.1734
0.8316
7.51E+05




SGDLSLVQ




EK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





93
P05317
78
33866
0.9997

1










RLA0_YEAST 60S acidic ribosomal protein P0 OS = Saccharomyces


cerevisiae GN = RPP0 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GTIEIVSDVK
X
0.9997
0
0.5768
0.9991
4.62E+06
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





94
P07257
78
40702


0










QCR2_YEAST Cytochrome b-c1 complex subunit 2, mitochondrial


OS = Saccharomyces cerevisiae GN = QCR2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





95
P46367
77
56688
0.916

1










ALDH4_YEAST Potassium-activated aldehyde dehydrogenase,


mitochondrial OS = Saccharomyces cerevisiae GN = ALD4 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IAPALVTGN
X
0.916
0.00158
0.04226
0.9968
5.28E+04




TVVLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





96
P16140
77
57713
0.5186

1










VATB_YEAST V-type proton ATPase subunit B OS = Saccharomyces


cerevisiae GN = VMA2 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
AIVQVFEG
X
0.5186
0.06922
0.03856
0.8934
1.27E+04




TSGIDVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





97
P39708
74
49596
0.9962

1










DHE5_YEAST NADP-specific glutamate dehydrogenase 2


OS = Saccharomyces cerevisiae GN = GDH3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
HIGKDTDV
X
0.9962
0.0039
0.09871
0.9621
8.21E+05




PAGDIGVG




GR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





98
P15992
74
23865


0










HSP26_YEAST Heat shock protein 26 OS = Saccharomyces cerevisiae


GN = HSP26 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
VITLPDYPG

0.1164
0.2258
0.295
0.3292
2.05E+05




VDADNIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





99
B3LP78
73
55768


0










BLH1_YEAS1 Cysteine proteinase 1, mitochondrial


OS = Saccharomyces cerevisiae (strain RM11-1a) GN = LAP3 PE = 3


SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





100
P32327
73
130638
0.6239
3.892
2










PYC2_YEAST Pyruvate carboxylase 2 OS = Saccharomyces cerevisiae


GN = PYC2 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
NFLAPAEP
X
0.894
0.01442
0.2074
0.9142
9.25E+05




DEEIEVTIE




QGK


2
3
DGESVDAS
X
0.09446
0.1607
0.3531
0.8345
1.76E+05




DLLVVLEEE




TLPPSQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





101
P37291
73
52186


0










GLYC_YEAST Serine hydroxymethyltransferase, cytosolic


OS = Saccharomyces cerevisiae GN = SHM2 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
LITSHLVDT

0.6945
0.07766
0.1892
0.388
1.35E+05




DPEVDSIIK




DEIER
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





102
P60010
73
41663
0.8046

1










ACT_YEAST Actin OS = Saccharomyces cerevisiae GN = ACT1 PE = 1


SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
QEYDESGP

0.674
0.07934
0.1333
0.5876
6.38E+04




SIVHHK


2
2
QEYDESGP
X
0.8046
0.02603
0.1087
0.8907
1.96E+05




SIVHHK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





103
P32582
72
56396


0










CBS_YEAST Cystathionine beta-synthase OS = Saccharomyces


cerevisiae GN = CYS4 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





104
P01095
71
8585


0










IPB2_YEAST Protease B inhibitors 2 and 1 OS = Saccharomyces


cerevisiae GN = PBI2 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
HNDVIENV

0.7575
0.01705
0.129
0.6437
5.58E+05




EEDKEVHTN
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





105
Q00955
71
250197
0.8507

1










ACAC_YEAST Acetyl-CoA carboxylase OS = Saccharomyces cerevisiae


GN = FAS3 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
QLSDGGLL
X
0.8507
0.01702
0.06509
0.973
1.45E+05




IAIGGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





106
P22203
70
26455


0










VATE_YEAST V-type proton ATPase subunit E OS = Saccharomyces


cerevisiae GN = VMA4 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EQSLDGIF

0.3294
0.1126
0.06772
0.6913
3.41E+04




EETK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





107
P38249
70
110276
0.9265

1










EIF3A_YEAST Eukaryotic translation initiation factor 3 subunit A


OS = Saccharomyces cerevisiae GN = TIF32 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TAGGSSPA
X
0.9265
0.00916
0.2441
0.9925
7.88E+04




TPATPATPA




TPTPSSGPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





108
P09435
69
70504


0










HSP73_YEAST Heat shock protein SSA3 OS = Saccharomyces


cerevisiae GN = SSA3 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





109
P32588
69
50758


0










PUB1_YEAST Nuclear and cytoplasmic polyadenylated RNA-binding


protein PUB1 OS = Saccharomyces cerevisiae GN = PUB1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
QYFQVGGP

0.9947
0.002
0.3581
0.3382
2.32E+05




IANIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





110
P53900
68
15171
0.05129

1










PFD4_YEAST Prefoldin subunit 4 OS = Saccharomyces cerevisiae


GN = GIM3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
NNTQVTFE
X
0.05129
0.3627
0.09004
0.7859
1.49E+05




DQQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





111
P40825
68
107940


0










SYAC_YEAST Alanyl-tRNA synthetase cytoplasmic


OS = Saccharomyces cerevisiae GN = ALA1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TFFETNEN

0.9828
0.00532
0.346
0.5419
8.94E+04




APYLVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





112
P38631
68
214712


0










FKS1_YEAST 1,3-beta-glucan synthase component FKS1


OS = Saccharomyces cerevisiae GN = FKS1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
ILAEETAAY

0.01026
1.465
0.2542
0.6992
1.23E+05




EGNENEAE




KEDALK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





113
P47079
67
61952


0










TCPQ_YEAST T-complex protein 1 subunit theta OS = Saccharomyces


cerevisiae GN = CCT8 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





114
P38205
66
78319


0










NCL1_YEAST tRNA (cytosine-5-)-methyltransferase NCL1


OS = Saccharomyces cerevisiae GN = NCL1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LSSETPALE

0.5913
0.04967
0.1079
0.3943
3.39E+05




SEGPQTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





115
P39939
65
13438


0










RS26B_YEAST 40S ribosomal protein S26-B OS = Saccharomyces


cerevisiae GN = RPS26B PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DLSEASVY

0.3176
0.05414
0.1397
0.3309
6.58E+05




PEYALPK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





116
P35189
64
27423
0.8078

1










TAF14_YEAST Transcription initiation factor TFIID subunit 14


OS = Saccharomyces cerevisiae GN = TAF14 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SGSTEETT
X
0.8078
0.02101
0.0963
0.9487
1.58E+04




ANTGTIGK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





117
Q08972
64
134247


0










NEW1_YEAST [NU+] prion formation protein 1 OS = Saccharomyces


cerevisiae GN = NEW1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
ASNLAKPS

0.3162
0.05206
0.143
0.3829
2.23E+05




VDDDDSPA




NIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





118
P05736
63
27392
0.622
1.054
2










RL2_YEAST 60S ribosomal protein L2 OS = Saccharomyces cerevisiae


GN = RPL2A PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
KVISSDAR
X
0.5777
0.00446
0.06036
0.9809
2.68E+04


2
3
ASLNVGNV
X
0.624
0.00764
0.308
0.9797
6.09E+05




LPLGSVPE




GTIVSNVE




EKPGDR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





119
P06367
61
14600


0










RS14A_YEAST 40S ribosomal protein S14-A OS = Saccharomyces


cerevisiae GN = RPS14A PE = 1 SV = 5

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





120
Q03195
60
68297
0.3246

1










RLI1_YEAST Translation initiation factor RLI1 OS = Saccharomyces


cerevisiae GN = RLI1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
FDDPPEWQ
X
0.3246
0.05303
0.04664
0.8258
2.37E+05




EIIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





121
P23638
60
28697


0










PSA4_YEAST Proteasome component Y13 OS = Saccharomyces


cerevisiae GN = PRE9 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





122
P33327
60
124254
0.9911
1.026
2










DHE2_YEAST NAD-specific glutamate dehydrogenase


OS = Saccharomyces cerevisiae GN = GDH2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GDIESISDK
X
1.001
0.00158
0.3693
0.9924
5.15E+05


2
2
LVSFWAPE
X
0.957
0.01189
0.05111
0.9876
1.49E+05




SELK


3
3
RNDTTLLEI

0.1906
0.2454
0.2091
0.5903
2.89E+04




VENLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





123
P17076
59
28107
0.7946

1










RL8A_YEAST 60S ribosomal protein L8-A OS = Saccharomyces


cerevisiae GN = RPL8A PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
YRPETAAEK
X
0.7946
0.00569
0.2624
0.987
1.02E+05


2
3
SKQDASPK

−0.000859
3.397
0.2839
0.2521
2.27E+05




PYAVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





124
P00815
58
87666


0










HIS2_YEAST Histidine biosynthesis trifunctional protein


OS = Saccharomyces cerevisiae GN = HIS4 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IKEEAEELT

0.1694
0.3439
0.09508
0.2327
1.01E+05




EAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





125
P02309
57
11361


0










H4_YEAST Histone H4 OS = Saccharomyces cerevisiae GN = HHF1 PE = 1


SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
DSVTYTEH

0.3491
0.08223
0.2286
0.1483
5.70E+05




AK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





126
P37299
57
8587
0.04592

1










QCR10_YEAST Cytochrome b-c1 complex subunit 10


OS = Saccharomyces cerevisiae GN = QCR10 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
IPLLGPTLE
X
0.04592
0.3578
0.08934
0.7487
1.68E+05




DHTPPEDK




PN
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





127
P23287
55
63355
1

1










PP2B1_YEAST Serine/threonine-protein phosphatase 2B catalytic


subunit A1 OS = Saccharomyces cerevisiae GN = CNA1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
ILNMSTVAL
X
1
0.001
0.05272
0.9692
2.68E+05




SKEPNLLKLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





128
P38011
54
34784
0.7242

1










GBLP_YEAST Guanine nucleotide-binding protein subunit beta-like


protein OS = Saccharomyces cerevisiae GN = ASC1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
VFSLDPQY
X
0.7242
0.00801
0.4127
0.9795
8.90E+05




LVDDLRPE




FAGYSK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





129
P53200
54
28564
0.5579

1










AML1_YEAST N(6)-adenine-specific DNA methyltransferase-like 1


OS = Saccharomyces cerevisiae GN = AML1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
EEQQHQEA
X
0.5579
0.1156
0.04329
0.7172
6.21E+04




FQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





130
P32190
52
80158


0










GLPK_YEAST Glycerol kinase OS = Saccharomyces cerevisiae GN = GUT1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





131
P19358
51
42470
0.9999

1










METK2_YEAST S-adenosylmethionine synthase 2 OS = Saccharomyces


cerevisiae GN = SAM2 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
TQLQKDIV
X
0.9999
0.00317
0.04256
0.7785
2.46E+05




EK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





132
Q12363
50
48353
0.7508

1










WTM1_YEAST Transcriptional modulator WTM1 OS = Saccharomyces


cerevisiae GN = WTM1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
YNPDDTIA
X
0.7508
0.002
0.7573
0.9978
2.44E+05




PPQDATEE




SQTK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





133
P31539
47
102533
0.8569

1










HS104_YEAST Heat shock protein 104 OS = Saccharomyces cerevisiae


GN = HSP104 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GADTNTPL
X
0.8569
0.01624
0.2723
0.9822
3.21E+05




EYLSK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





134
P39935
46
107036
0.815

1










IF4F1_YEAST Eukaryotic initiation factor 4F subunit p150


OS = Saccharomyces cerevisiae GN = TIF4631 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
LKETSDST
X
0.815
0.05328
0.1577
0.8433
8.82E+04




STSTPTPTP




STNDSK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





135
P35732
46
83923
0.9125

1










YKF4_YEAST Uncharacterized protein YKL054C OS = Saccharomyces


cerevisiae GN = YKL054C PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
EQVKEEEQ
X
0.9125
0.02943
0.623
0.9847
1.75E+05




TAEELEQE




QDNVAAPE




EEVTVVEEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





136
P17255
45
119131


0










VATA_YEAST V-type proton ATPase catalytic subunit A


OS = Saccharomyces cerevisiae GN = TFP1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





137
P02294
45
14229
0.8421

1










H2B2_YEAST Histone H2B.2 OS = Saccharomyces cerevisiae GN = HTB2


PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
QTHPDTGI
X
0.8421
0.00914
0.1463
0.9218
1.30E+05




SQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





138
P02293
45
14244
0.8421

1










H2B1_YEAST Histone H2B.1 OS = Saccharomyces cerevisiae GN = HTB1


PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
QTHPDTGI
X
0.8421
0.00914
0.1463
0.9218
1.30E+05




SQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





139
P05749
43
13789


0










RL22A_YEAST 60S ribosomal protein L22-A OS = Saccharomyces


cerevisiae GN = RPL22A PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





140
P40204
43
8477
1

1










RUXG_YEAST Small nuclear ribonucleoprotein G OS = Saccharomyces


cerevisiae GN = SMX2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
KVAGILR
X
1
0
0.07689
0.9937
4.35E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





141
P08518
43
139256


0










RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2


OS = Saccharomyces cerevisiae GN = RPB2 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





142
P05755
43
22421


0










RS9B_YEAST 40S ribosomal protein S9-B OS = Saccharomyces


cerevisiae GN = RPS9B PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





143
Q01855
43
15992


0










RS15_YEAST 40S ribosomal protein S15 OS = Saccharomyces


cerevisiae GN = RPS15 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LLEMSTED

0.384
0.05738
0.2239
0.6167
5.45E+05




FVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





144
P26781
42
17898
1

1










RS11_YEAST 40S ribosomal protein S11 OS = Saccharomyces


cerevisiae GN = RPS11A PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
1
NAGLGFK
X
1
0
0.701
0.9998
2.17E+06
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





145
P00950
42
27784


0










PMG1_YEAST Phosphoglycerate mutase 1 OS = Saccharomyces


cerevisiae GN = GPM1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





146
P32380
41
112692
0.9554

1










NUF1_YEAST Protein NUF1 OS = Saccharomyces cerevisiae GN = NUF1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IIDLQKK

0.9984
0.00413
0.00899
0.6498
1.06E+04


2
2
IEIENWK
X
0.9554
0.01028
0.1168
0.9842
1.57E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





147
P16120
41
57439


0










THRC_YEAST Threonine synthase OS = Saccharomyces cerevisiae


GN = THR4 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
LYIAQEEIP

0.04854
0.3108
0.1234
0.3822
1.17E+06




DADLKDLIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





148
P43616
41
52838
0.6185

1










DUG1_YEAST Cys-Gly metallodipeptidase DUG1 OS = Saccharomyces


cerevisiae GN = DUG1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ILIDGIDEM
X
0.6185
0.00821
0.1115
0.9559
3.58E+04




VAPLTEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





149
P25294
38
37567
0.5309

1










SIS1_YEAST Protein SIS1 OS = Saccharomyces cerevisiae GN = SIS1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
YHPDKPTG
X
0.5309
0.05698
0.03541
0.7338
2.13E+05




DTEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





150
P0C0T4
37
12002
0.8113

1










RS25B_YEAST 40S ribosomal protein S25-B OS = Saccharomyces


cerevisiae GN = RPS25B PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
AQHAVILD
X
0.8113
0.04438
0.03423
0.7174
2.04E+04




QEK


2
3
AQHAVILD

0.1884
0.06967
0.3797
0.1743
2.54E+06




QEKYDR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





151
Q08438
37
73997


0










VHS3_YEAST Protein VHS3 OS = Saccharomyces cerevisiae GN = VHS3


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





152
Q0550
36
69890


0










SYRC_YEAST Arginyl-tRNA synthetase, cytoplasmic


OS = Saccharomyces cerevisiae GN = YDR341C PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
YGNEEALVK

0.1829
0.1367
0.1933
0.1382
3.93E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





153
P06168
36
44565


0










ILV5_YEAST Ketol-acid reductoisomerase, mitochondrial


OS = Saccharomyces cerevisiae GN = ILV5 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





154
P38167
36
123534
0.5931

1










ECM21_YEAST Protein ECM21 OS = Saccharomyces cerevisiae


GN = ECM21 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SRFNNLDK
X
0.5931
0.03207
0.03169
0.8355
1.66E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





155
P04076
34
52173


0










ARLY_YEAST Argininosuccinate lyase OS = Saccharomyces cerevisiae


GN = ARG4 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





156
P61864
33
8552
0.8436

1










UBIQ_YEAST Ubiquitin OS = Saccharomyces cerevisiae GN = UBI1 PE = 1


SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IQDKEGIPP
X
0.8436
0.00578
0.2069
0.9679
1.11E+06




DQQR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





157
P54839
33
55324


0










HMCS_YEAST Hydroxymethylglutaryl-CoA synthase


OS = Saccharomyces cerevisiae GN = ERG13 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





158
P40482
33
103842


0










SEC24_YEAST Protein transport protein SEC24 OS = Saccharomyces


cerevisiae GN = SEC24 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





159
P05694
31
85807
0










METE_YEAST 5-methyltetrahydropteroyltriglutamate--homocysteine


methyltransferase OS = Saccharomyces cerevisiae GN = MET6 PE = 1


SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
APEQFDEV

0.8993
0.03287
0.3114
0.6099
7.32E+05




VAAIGNK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





160
P0C0W1
31
14705


0










RS22A_YEAST 40S ribosomal protein S22-A OS = Saccharomyces


cerevisiae GN = RPS22A PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





161
P06105
30
135689


0










SC160_YEAST Protein SCP160 OS = Saccharomyces cerevisiae


GN = SCP160 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
FQFLIDAEE

0.2574
0.1495
0.03011
0.4086
8.22E+3004




LKEK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





162
P14065
30
35057
0.8654

1










GCY_YEAST Protein GCY OS = Saccharomyces cerevisiae GN = GCY1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GYVVLPK
X
0.8654
0.0811
0.06444
0.8822
3.00E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





163
P52490
29
17561


0










UBC13_YEAST Ubiquitin-conjugating enzyme E2 13


OS = Saccharomyces cerevisiae GN = UBC13 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





164
P38994
28
89754


0










MSS4_YEAST Probable phosphatidylinositol-4-phosphate 5-kinase


MSS4 OS = Saccharomyces cerevisiae GN = MSS4 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ISAVTATST

−0.000063
7.067
0.305
0.9995
4.66E+05




TIK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





165
P32893
28
63328


0










KRE11_YEAST Beta-glucan synthesis-associated protein KRE11


OS = Saccharomyces cerevisiae GN = KRE11 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ASEQLTKK

0.3303
0.2361
0.02043
0.1669
9586
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





166
A6ZPZ1
28
95169
0.999

1










YJ00_YEAS7 UPF0508 protein SCY_2952 OS = Saccharomyces


cerevisiae (strain YJM789) GN = SCY_2952 PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SIQVPLSPK
X
0.999
0.00323
0.07993
0.9881
3.06E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





167
P15891
28
65536


0










ABP1_YEAST Actin-binding protein OS = Saccharomyces cerevisiae


GN = ABP1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
AEAPKPEV

0.2106
0.08472
0.3799
0.4288
9.13E+05




PEDEPEGE




PDVK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





168
P32074
27
105239
0.8225

1










COPG_YEAST Coatomer subunit gamma OS = Saccharomyces


cerevisiae GN = SEC21 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
SETTLDTTP
X
0.8225
0.02368
0.1323
0.7806
1.44E+05




EAESVPEKR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





169
P04801
27
84987


0










SYTC_YEAST Threonyl-tRNA synthetase, cytoplasmic


OS = Saccharomyces cerevisiae GN = THS1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





170
B3RHV0
27
28726
0.954

1










RS3A1_YEAS1 40S ribosomal protein S1-A OS = Saccharomyces


cerevisiae (strain RM11-1a) GN = RPS1A PE = 3 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LRVDEVQGK
X
0.954
0.00845
0.1571
0.9013
1.03E+06
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





171
Q01217
27
95307


0










ARG56_YEAST Protein ARG5,6, mitochondrial OS = Saccharomyces


cerevisiae GN = ARG5, 6 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





172
P32861
27
56234
0.7068

1










UGPA1_YEAST UTP--glucose-1-phosphate uridylyltransferase


OS = Saccharomyces cerevisiae GN = UGP1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
YEIISQQPE
X
0.7068
0.00158
0.1676
0.9848
2.66E+05




NVSNLSK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





173
Q12462
27
26995


0










PEX11_YEAST Peroxisomal membrane protein PMP27


OS = Saccharomyces cerevisiae GN = PEX11 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





174
P53583
27
61628
0.9997

1










MPA43_YEAST Protein MPA43 OS = Saccharomyces cerevisiae


GN = MPA43 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ALQKCLQK
X
0.9997
0
0.5408
0.9792
4.03E+05




LNIR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





175
P38737
26
211316
1

1










ECM29_YEAST Proteasome component ECM29 OS = Saccharomyces


cerevisiae GN = ECM29 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LKNLLR
X
1
0
0.07689
0.9937
4.35E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





176
P40494
26
90976
1

1










PRK1_YEAST Actin-regulating kinase PRK1 OS = Saccharomyces


cerevisiae GN = PRK1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LKNLIR
X
1
0
0.07689
0.9937
4.35E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





177
P36048
26
114578
1

1










SN114_YEAST 114 kDa U5 small nuclear ribonucleoprotein component


OS = Saccharomyces cerevisiae GN = SNU114 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LKNLLR
X
1
0
0.07689
0.9937
4.35E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





178
Q01846
26
130637
0.08842

1










MDM1_YEAST Structural protein MDM1 OS = Saccharomyces cerevisiae


GN = MDM1 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TKIYIR
X
0.08842
0.1027
0.1197
0.9815
7.92E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





179
P04456
26
15924


0










RL25_YEAST 60S ribosomal protein L25 OS = Saccharomyces


cerevisiae GN = RPL25 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





180
Q99186
24
55352
1.007

1










AP2M_YEAST AP-2 complex subunit mu OS = Saccharomyces cerevisiae


GN = APM4 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
HSGSDFGNK
X
1.007
0.00775
0.03715
0.9671
4599
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





181
Q04922
23
53135
0.9994

1










MFB1_YEAST Mitochondrial F-box protein MFB1 OS = Saccharomyces


cerevisiae GN = MFB1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
KDNPRLK
X
0.9994
0.00158
0.4699
0.9983
3.45E+06
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





182
Q03786
23
22353


0










GNTK_YEAST Probable gluconokinase OS = Saccharomyces cerevisiae


GN = YDR248C PE = 1 SV = 1




















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
KYRDLIR

0.000004
1211
0.06617
0.9937
3.09E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





183
P04147
23
64304


0










PABP_YEAST Polyadenylate-binding protein, cytoplasmic and nuclear


OS = Saccharomyces cerevisiae GN = PAB1 PE = 1 SV = 4

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
YQGVNLFVK

0.6493
0.04431
0.1257
0.2785
2.62E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





184
P13663
23
39519


0










DHAS_YEAST Aspartate-semialdehyde dehydrogenase


OS = Saccharomyces cerevisiae GN = HOM2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IREDPLLDFK

0.18
0.182
0.08109
0.1847
7.16E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





185
P19097
23
207964


0










FAS2_YEAST Fatty acid synthase subunit alpha OS = Saccharomyces


cerevisiae GN = FAS2 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





186
P38264
23
21123


0










PHO88_YEAST Inorganic phosphate transport protein PHO88


OS = Saccharomyces cerevisiae GN = PHO88 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SALEHNEVK

0.942
0.01455
0.09329
0.575
5.32E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





187
P33203
23
69023
0.9927

1










PRP4O_YEAST Pre-mRNA-processing protein PRP40


OS = Saccharomyces cerevisiae GN = PRP40 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
YLSNRSAD
X
0.9927
0.00412
0.2098
0.996
4.72E+04




QLLK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





188
P32386
22
189043


0










YBT1_YEAST ATP-dependent bile acid permease OS = Saccharomyces


cerevisiae GN = YBT1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
IFNMILNK

0.004101
0.9579
0.2443
0.5181
1.15E+06
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





189
P40075
22
26909


0










SCS2_YEAST Vesicle-associated membrane protein-associated protein


SCS2 OS = Saccharomyces cerevisiae GN = SCS2 PE = 1 SV = 3

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
YLISPDVHP

0.6453
0.1021
0.2303
0.4558
6.49E+04




AQNQNIQE




NK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





190
Q06685
22
129674
1.008

1










VIP1_YEAST Inositol hexakisphosphate and diphosphoinositol-


pentakisphosphate kinase OS = Saccharomyces cerevisiae GN = VIP1


PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SSTSHPKPR
X
1.008
0.02117
0.06128
0.7799
7778
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





191
P46962
21
38057


0










CTK2_YEAST CTD kinase subunit beta OS = Saccharomyces cerevisiae


GN = CTK2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





192
P13188
21
93075
0.9115

1










SYQ_YEAST Glutaminyl-tRNA synthetase OS = Saccharomyces


cerevisiae GN = GLN4 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SDFSENVD
X
0.9115
0.00801
0.1843
0.8822
6.60E+05




DKEFFR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





193
Q02208
21
86313
0.9576

1










TOF2_YEAST Topoisomerase 1-associated factor 2


OS = Saccharomyces cerevisiae GN = TOF2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
AESKDLDL
X
0.9576
0.00992
0.5313
0.8332
4.35E+06




LR
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





194
P43544
21
25116
0.9621

1










SNO3_YEAST Probable glutamine amidotransferase SNO3


OS = Saccharomyces cerevisiae GN = SNO3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LDGKDNG
X
0.9621
0.00918
0.1046
0.9559
1.74E+05




GQELIVAAK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





195
P53254
21
141262


0










UTP22_YEAST U3 small nucleolar RNA-associated protein 22


OS = Saccharomyces cerevisiae GN = UTP22 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
LSERLTLAQ

0.002931
1.18
0.313
0.9968
1.09E+06




YK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





196
Q12507
21
38997
0.9995

1










SFG1_YEAST Superficial pseudohyphal growth protein 1


OS = Saccharomyces cerevisiae GN = SFG1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TSSKNVK
X
0.9995
0.00158
0.4979
0.9993
2.25E+06
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





197
Q06625
20
175551


0










GDE_YEAST Glycogen debranching enzyme OS = Saccharomyces


cerevisiae GN = GDB1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





198
P17555
20
57486
0.7116

1










CAP_YEAST Adenylyl cyclase-associated protein OS = Saccharomyces


cerevisiae GN = SRV2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SDGGNIYL
X
0.7116
0.00648
0.07351
0.9734
7.93E+04




SK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





199
Q12345
20
28402


0










IES3_YEAST Ino eighty subunit 3 OS = Saccharomyces cerevisiae


GN = IES3 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
IDILTKIQE

0.7775
0.1023
0.03577
0.4115
952.5




NLLEEYQK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





200
P32802
20
75914
0.9962

1










TMN1_YEAST Transmembrane 9 superfamily member 1


OS = Saccharomyces cerevisiae GN = EMP70 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
KIYSSIK
X
0.9962
0.02516
0.03919
0.9666
1.24E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





201
P53295
20
40980
0.9333

1










YG3Y_YEAST Uncharacterized GTP-binding protein YGR173W


OS = Saccharomyces cerevisiae GN = YGR173W PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
3
CLYVYNKI
X
0.9333
0.01137
0.1522
0.9687
5.58E+05




DAVSLEEV




DK
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





202
P53244
20
65724
0.03843

1










ART5_YEAST Arrestin-related trafficking adapter 5


OS = Saccharomyces cerevisiae GN = ART5 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
GRLVLFDK
X
0.03843
0.07779
0.03009
0.8963
8.52E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





203
P53598
20
35010
0.9917

1










SUCA_YEAST Succinyl-CoA ligase [ADP-forming] subunit alpha,


mitochondrial OS = Saccharomyces cerevisiae GN = LSC1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
ESIPYDK
X
0.9917
0.001
0.4495
0.9852
2.95E+06
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





204
P48524
19
109107.00


0










BUL1_YEAST Ubiquitin ligase-binding protein BUL1


OS = Saccharomyces cerevisiae GN = BUL1 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
SPSLHSPK

0.5209
0.06221
0.06108
0.3577
1.00E+05
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





205
P35172
19
89623


0










TREB_YEAST Probable trehalase OS = Saccharomyces cerevisiae


GN = NTH2 PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
RAFRAAIK

0.05024
0.1466
0.00365
0.2201
1.25E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





206
P10963
18
61201


0










PCKA_YEAST Phosphoenolpyruvate carboxykinase [ATP]


OS = Saccharomyces cerevisiae GN = PCK1 PE = 1 SV = 2

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





207
P53133
18
30896
0.8643

1










YGL7_YEAST Uncharacterized protein YGL117W OS = Saccharomyces


cerevisiae GN = YGL117W PE = 1 SV = 1

















z
Sequence
Incl.
L/(L + H)
Std. Err.
Fraction
Correlation
Intensity
Modifications





1
2
TSLKITHRR
X
0.8643
0.01604
0.0279
0.7852
9.11E+04
















Hit
Accession
Score
Mass
L/(L + H)
SD(geo)
#





208
Q07913
17
38310


0










NSE1_YEAST Non-structural maintenance of chromosomes element 1


OS = Saccharomyces cerevisiae GN = NSE1 PE = 1 SV = 1













TABLE 3







Ribosomal proteins used to establish the non-specifically associating baseline for ChAP-MS


analyses. The percentage light and standard deviation are listed for each ribosomal protein.













Stdev

Stdev


Ribosomal Proteins
Glucose
Glucose
Galactose
Galactose














40S ribosomal protein S10-A OS = Saccharomyces cerevisiae GN = RPS10A
48.01%
1.14%
65.47%
0.00%


PE = 1 SV = 1


40S ribosomal protein S17-A OS = Saccharomyces cerevisiae GN = RPS17A
47.77%
0.00%
70.60%
4.47%


PE = 1 SV = 1


40S ribosomal protein S21-A OS = Saccharomyces cerevisiae GN = RPS21A
53.30%
1.79%
56.17%
1.13%


PE = 1 SV = 1


60S ribosomal protein L14-B OS = Saccharomyces cerevisiae GN = RPL14B
52.21%
4.40%
77.37%
10.01%


PE = 1 SV = 1


60S ribosomal protein L19 OS = Saccharomyces cerevisiae GN = RPL19A PE = 1
50.26%
1.25%
71.05%
5.03%


SV = 5


60S ribosomal protein L26-A OS = Saccharomyces cerevisiae GN = RPL26A
51.09%
0.00%
70.20%
0.00%


PE = 1 SV = 3


60S ribosomal protein L3 OS = Saccharomyces cerevisiae GN = RPL3 PE = 1
49.39%
5.09%
66.83%
7.02%


SV = 4


60S ribosomal protein L30 OS = Saccharomyces cerevisiae GN = RPL30 PE = 1
48.85%
4.03%
62.85%
4.95%


SV = 3


40S ribosomal protein S12 OS = Saccharomyces cerevisiae GN = RPS12 PE = 1
50.92%
13.06%
78.21%
1.50%


SV = 1


40S ribosomal protein S19-A OS = Saccharomyces cerevisiae GN = RPS19A
49.03%
1.43%
59.47%
1.64%


PE = 1 SV = 2


40S ribosomal protein S26-A OS = Saccharomyces cerevisiae GN = RPS26A
50.63%
2.36%
71.70%
4.02%


PE = 1 SV = 1


40S ribosomal protein S4 OS = Saccharomyces cerevisiae GN = RPS4A PE = 1
44.54%
11.51%
54.31%
4.61%


SV = 3


40S ribosomal protein S7-A OS = Saccharomyces cerevisiae GN = RPS7A
51.87%
2.38%
75.86%
6.19%


PE = 1 SV = 4


40S ribosomal protein S11 OS = Saccharomyces cerevisiae GN = RPS11A
49.48%
3.94%
74.42%
3.71%


PE = 1 SV = 3


60S acidic ribosomal protein P0 OS = Saccharomyces cerevisiae GN = RPP0
50.01%
2.91%
62.25%
3.64%


PE = 1 SV = 1


60S ribosomal protein L10 OS = Saccharomyces cerevisiae GN = RPL10 PE = 1
53.45%
2.89%
63.81%
2.66%


SV = 1


60S ribosomal protein L12 OS = Saccharomyces cerevisiae GN = RPL12A PE = 1
51.79%
1.15%
66.76%
2.02%


SV = 1


60S ribosomal protein L30 OS = Saccharomyces cerevisiae GN = RPL30 PE = 1
48.85%
4.03%
63.49%
4.82%


SV = 3


60S ribosomal protein L9-A OS = Saccharomyces cerevisiae GN = RPL9A PE = 1
49.58%
3.07%
58.70%
2.73%


SV = 2


40S ribosomal protein S1-B OS = Saccharomyces cerevisiae (strain YJM789)
47.63%
4.27%
75.33%
9.16%


GN = RPS1B PE = 3 SV = 1
















TABLE 4







Proteins and PTMs specifically associating with GAL1 chromatin isolated from


cells cultured in galactose. Proteins and histone posttranslational modifications listed


are greater than two standard deviations from the non-specific threshold (80.9% Light).










% Light
Stdev


Protein Name
Glucose
Glucose












DNA-directed RNA polymerase II 140 kDa polypeptide (EC 2.7.7.6) (B150) - S cerevisiae
100.00%
0.00%


Histone H3K18acK23ac
100.00%
0.00%


Histone H2A.1 OS = Saccharomyces cerevisiae GN = HTA1 PE = 1 SV = 2
97.10%
6.02%


NAD-specific glutamate dehydrogenase OS = Saccharomyces cerevisiae GN = GDH2 PE = 1 SV = 1
96.09%
2.70%


Histone H4K5acK8ac
95.89%
0.00%


DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) (RNA polymerase II subunit 1) (B220) - S
94.36%
4.99%


cerevisiae


Histone H3K9acK14ac
93.62%
0.00%


Histone H4K12acK16ac
90.56%
3.00%


Histone H2B.1 OS = Saccharomyces cerevisiae GN = HTB1 PE = 1 SV = 2
89.59%
9.51%


Acetyl-CoA carboxylase OS = Saccharomyces cerevisiae GN = FAS3 PE = 1 SV = 2
89.04%
3.39%


6-phosphogluconate dehydrogenase, decarboxylating 1 OS = Saccharomyces cerevisiae GN = GND1 PE = 1
87.74%
3.05%


SV = 1


Probable inosine-5′-monophosphate dehydrogenase IMD3 OS = Saccharomyces cerevisiae GN = IMD3
87.19%
14.00%


PE = 1 SV = 1


Eukaryotic translation initiation factor 3 subunit A OS = Saccharomyces cerevisiae GN = TIF32 PE = 1 SV = 1
86.97%
7.61%


Histone H3K14ac
85.83%
4.48%


Histone H3 OS = Saccharomyces cerevisiae GN = HHT1 PE = 1 SV = 2
85.83%
4.48%


Zuotin OS = Saccharomyces cerevisiae GN = ZUO1 PE = 1 SV = 1
85.33%
5.43%


Protein GCY OS = Saccharomyces cerevisiae GN = GCY1 PE = 1 SV = 1
85.18%
7.02%


Histone H4 OS = Saccharomyces cerevisiae GN = HHF1 PE = 1 SV = 2
90.42%
8.84%


Actin-related protein 2/3 complex subunit 4 OS = Saccharomyces cerevisiae GN = ARC19 PE = 1 SV = 2
84.74%
4.60%


Translationally-controlled tumor protein homolog OS = Saccharomyces cerevisiae GN = TMA19 PE = 1 SV = 1
84.64%
1.50%


Suppressor protein STM1 OS = Saccharomyces cerevisiae GN = STM1 PE = 1 SV = 3
84.58%
5.36%


FACT complex subunit SPT16 OS = Saccharomyces cerevisiae GN = SPT16 PE = 1 SV = 1
84.24%
3.60%


Hexokinase-2 OS = Saccharomyces cerevisiae GN = HXK2 PE = 1 SV = 4
84.22%
5.92%


Alcohol dehydrogenase 1 OS = Saccharomyces cerevisiae GN = ADH1 PE = 1 SV = 4
83.55%
11.23%


Pyruvate carboxylase 1 OS = Saccharomyces cerevisiae GN = PYC1 PE = 1 SV = 2
82.51%
7.74%


Protein GAL3 OS = Saccharomyces cerevisiae GN = GAL3 PE = 1 SV = 2
81.95%
8.37%


Cell division control protein 48 OS = Saccharomyces cerevisiae GN = CDC48 PE = 1 SV = 3
80.99%
2.13%
















TABLE 5







Proteins and PTMs specifically associating with GAL1 chromatin isolated from


cells cultured in glucose. Proteins and histone posttranslational modifications listed are


greater than two standard deviations from the non-specific threshold (56.18% Light).










% Light
Stdev


Protein Name
Glucose
Glucose












Histone H3K36me3
100.00%
0.00%


Glucose-6-phosphate isomerase OS = Saccharomyces cerevisiae GN = PGI1 PE = 1 SV = 3
66.33%
12.98%


Magnesium-activated aldehyde dehydrogenase, cytosolic OS = Saccharomyces cerevisiae GN = ALD6
58.78%
9.50%


PE = 1 SV = 4


Phosphoglycerate mutase 1 OS = Saccharomyces cerevisiae GN = GPM1 PE = 1 SV = 3
58.62%
6.39%


Plasma membrane ATPase 1 OS = Saccharomyces cerevisiae GN = PMA1 PE = 1 SV = 2
58.47%
6.81%


Cystathionine gamma-lyase OS = Saccharomyces cerevisiae GN = CYS3 PE = 1 SV = 2
58.10%
3.72%


Enolase 1 OS = Saccharomyces cerevisiae GN = ENO1 PE = 1 SV = 2
57.88%
2.93%


Enolase 2 OS = Saccharomyces cerevisiae GN = ENO2 PE = 1 SV = 2
57.40%
2.33%


Heat shock protein SSA4 OS = Saccharomyces cerevisiae GN = SSA4 PE = 1 SV = 3
56.99%
4.82%


Cell division control protein 48 OS = Saccharomyces cerevisiae GN = CDC48 PE = 1 SV = 3
56.59%
4.13%


Hexokinase-2 OS = Saccharomyces cerevisiae GN = HXK2 PE = 1 SV = 4
56.50%
3.43%


Fatty acid synthase subunit alpha OS = Saccharomyces cerevisiae GN = FAS2 PE = 1 SV = 2
56.19%
6.29%
















TABLE 6







TAL protein DNA-binding specificity. ChIP was performed for the TAL-PrA


used in this study and relative genomic binding was measured with qPCR at each


sequence listed below.


Real time qPCR primers were used to amplify regions containing the indicated sequences and


enrichment of each was measured relative to ACT1. The standard error of three analyses is shown. The


first listed DNA sequence at GAL1 (highlighted gray) was used to design the TAL protein. A BLAST 


search was used to identify the next five closest binding sites in the S. cerevisiae genome.  


Mismatches of these five sequences relative to the GAL1 sequence are shown in bold.

















ChIP-qPCR for



Chromo-

Closest

TAL-PrA binding


Sequence
some
Coordinates
Gene
Locus tag
Relative to Actin









ChrII
278829-278846
GAL1
YBR020W, promoter  region
6.14 ± 0.28


GGGGTAATTAATCATTTT
ChrIV
823079-823066
SCC2
YDR180W
0.65 ± 0.06


TTATACATTAATCAGCGA
ChrXV
18844-18855
ENB1
between YOL159C and
1.34 ± 0.13






YOL158C



GGGGTAATTAATGTAAAT
ChrXIV
614716-614705
IDP3
YNL009W, promoter 
0.94 ± 0.46






region



AAATTAATCAGCGGTGAC
ChrIX
88064-88053
REV7
YIL139C
0.77 ± 0.27


GGGGTAATTAAAATTTCT
ChrXVI
94211-94221
IQG1
YPL242C
0.76 ± 0.10
















TABLE 7







Significant proteins (>2-fold enriched) identified with GAL1 promoter chromatin


from cells grown in galactose-containing media. The top 10% of proteins that are >15-


fold enriched are highlighted in gray.















Spectral





Spectral
Counts




Molecular
Counts
Wild


Proteins

Weight
TAL-PrA
type









PMA1_YEAST
99,621.60
558
0


 






YH11B_YEAST (+2)
202,825.20
273
0


 






DED1_YEAS7 (+1)
65,554.50
261
0


 






TIF31 YEAST
145,171.10
226
0


 






PYR1_YEAST
245,129.90
1356
3


 






EF3B_YEAST
115,871.60
220
0


 






YO11A_YEAST
49,006.10
216
0


 






RS3A2_YEAS1 (+3)
28,812.90
204
0


 






RS3A1_YEAS1 (+4)
28,743.60
189
0


 






YD12A_YEAST
49,187.40
188
0


 






GAL2_YEAST
63,627.00
183
0


 






ASSY_YEAST
46,941.00
177
0


 






PDR5_YEAST
170,444.10
152
0


 






FKS1_YEAST
214,859.40
151
0


 






HSP7E_YEAST
70,086.90
150
0


 






PDC6_YEAST
61,582.40
150
0


 






BFR1_YEAST
54,641.70
137
0


 






RL18_YEAST
20,563.70
129
0


 






RS2_YEAST
27,450.20
126
0


 






FKS2_YEAST
216,998.10
126
0


 






6PGD2_YEAST
53,925.30
118
0


 






HXT7_YEAST
62,736.00
108
0


 






GAL3_YEAST
58,130.40
107
0


 






MS116_YEAST
76,272.50
105
0


 






ATC6_YEAST
135,274.80
98
0


 






HXT6_YEAST
62,706.00
98
0


 






IF2P_YEAST
112,271.50
98
0


 






RPB1_YEAST
191,615.10
96
0


 






GAS1_YEAST
59,583.20
94
0


 






EIF3B_YEAS7
88,131.50
93
0


 






PGM1_YEAST
63,114.70
91
0


 






TCPG_YEAST
58,814.70
90
0


 






SPT16_YEAST
118,636.00
88
0


 






DBP1_YEAS7 (+1)
67,992.10
87
0


 






ODP2_YEAST
51,819.70
87
0


 






CLH_YEAST
187,243.20
173
1


 






RS8_YEAST
22,490.40
86
0


 






RPB2_YEAST
138,757.20
85
0


 






GLNA_YEAST
41,767.10
80
0


 






TOM40_YEAST
42,039.40
79
0


 






C1TC_YEAST
102,207.30
76
0


 






FBRL_YEAST
34,365.50
75
0


 






SC160_YEAST
134,813.70
300
2


 






SEC23_YEAST
85,387.60
73
0


 






NOP56_YEAST
56,867.30
73
0


 






PYRF_YEAST
29,240.40
71
0


 






HOSC_YEAST
47,100.30
68
0


 






NDH1_YEAST
62,776.50
67
0


 






EIF3C_YEAS7
93,225.20
67
0


 






ZUO1_YEAST
49,021.50
66
0


 






TPS2_YEAST
102,978.90
63
0


 






RRP5_YEAST
193,141.40
63
0


 






RRP5_YEAST
193,141.40
63
0


 






KAPR_YEAST
47,220.30
62
0


 











Galactokinase OS = Saccharomyces cerevisiae GN = GAL1 PE = 1 SV = 4
GAL1_YEAST
57,945.00
1350
11


Probable 2-methylcitrate dehydratase OS = Saccharomyces cerevisiae
PRPD_YEAST
57,685.70
61
0


GN = PDH1 PE = SV = 1






2-isopropylmalate synthase 2, mitochondrial OS = Saccharomyces
LEU9_YEAST
67,201.00
61
0


cerevisiae GN = LEU9 PE = SV = 1






NADH-cytochrome b5 reductase 2 OS = Saccharomyces cerevisiae
MCR1_YEAS7
34,109.10
61
0


(strain YJM789) GN = MCR1 PE = 2 SV = 1
(+1)





6,7-dimethyl-8-ribitylumazine synthase OS = Saccharomyces
RIB4_YEAST
18,555.70
60
0


cerevisiae GN = RIB4 PE = 1 SV = 2






N-(5′-phosphoribosyl)anthranilate isomerase OS = Saccharomyces
TRPF_YEAST
24,144.90
60
0


cerevisiae GN = TRP1 PE = 1 SV = 2






Glutamate synthase [NADH] OS = Saccharomyces cerevisiae
GLT1_YEAST
238,108.30
58
0


GN = GLT1 PE = 1 SV = 2






Nuclear localization sequence-binding protein OS = Saccharomyces
NSR1_YEAST
44,536.10
55
0


cerevisiae GN = NSR1 PE = 1 SV = 1






V-type proton ATPase subunit a, vacuolar isoform
VPH1_YEAST
95,533.10
55
0


OS = Saccharomyces cerevisiae GN = VPH1 PE = 1 SV = 3






4-aminobutyrate aminotransferase OS = Saccharomyces cerevisiae
GATA_YEAST
52,948.60
55
0


GN = UGA1 PE = 1 SV = 2






Dihydroorotate dehydrogenase OS = Saccharomyces cerevisiae
PYRD_YEAST
34,802.70
54
0


GN = URA1 PE = 1 SV = 1






Eukaryotic translation initiation factor 2A OS = Saccharomyces
EIF2A_YEAST
71,307.10
54
0


cerevisiae GN = YGR054W PE = 1 SV = 1






60S ribosomal protein L32 OS = Saccharomyces cerevisiae GN = RPL32
RL32_YEAST
14,771.80
53
0


PE = SV = 1






60S ribosomal protein L15-A OS = Saccharomyces cerevisiae
RL15A_YEAST 
24,422.60
105
1


GN = RPL15A PE = 1 SV = 3






Mitochondrial import receptor subunit TOM70 OS = Saccharomyces
TOM70_YEAS7
70,127.70
51
0


cerevisiae (strain YJM789) GN = TOM70 PE = 3 SV = 1
(+1)





Mitochondrial acidic protein MAM33 OS = Saccharomyces cerevisiae
MAM33_YEAST
30,132.70
51
0


GN = MAM33 PE = 1 SV = 1






H/ACA ribonucleoprotein complex subunit 4 OS = Saccharomyces
CBF5_YEAST
54,706.30
51
0


cerevisiae GN = CBF5 PE = 1 SV = 1






60S ribosomal protein L8-A OS = Saccharomyces cerevisiae
RL8A_YEAST
28,125.50
201
2


GN = RPL8A PE = 1 SV = 4






Eukaryotic translation initiation factor 2 subunit alpha
IF2A_YEAST
34,718.70
50
0


OS = Saccharomyces cerevisiae GN = SUI2 PE = SV = 1






NADPH--cytochrome P450 reductase OS = Saccharomyces cerevisiae
NCPR_YEAST
76,774.20
50
0


GN = NCP1 PE = 1 SV = 3






Nucleolar protein 58 OS = Saccharomyces cerevisiae (strain YJM789)
NOP58_YEAS7
56,959.80
98
1


GN = NOP58 PE = 3 SV = 1
(+1)





60S ribosomal protein L14-B OS = Saccharomyces cerevisiae
RL148B_YEAST
15,153.20
97
1


GN = RPL14B PE = 1 SV = 1






Pentafunctional AROM polypeptide OS = Saccharomyces cerevisiae
ARO1_YEAST
174,758.00
97
1


GN = ARO1 PE = 1 SV = 1






60S ribosomal protein L8-B OS = Saccharomyces cerevisiae
RL8B_YEAST
28,112.80
193
2


GN = RPL8B PE = 1 SV = 3






GTP-binding protein RHO1 OS = Saccharomyces cerevisiae GN = RHO1
RHO1_YEAST
23,152.00
48
0


PE = 1 SV = 3






Invertase 2 OS = Saccharomyces cerevisiae GN = SUC2 PE = 1 SV = 1
INV2_YEAST
60,641.00
48
0



(+1)





Squalene synthase OS = Saccharomyces cerevisiae GN = ERG9 PE = 1
FDFT_YEAST
51,722.50
48
0


SV = 2






Eukaryotic translation initiation factor 3 subunit B OS = Saccharomyces
EIF3B_YEAST
88,131.50
95
1


cerevisiae GN = PRT1 PE = 1 SV = 1






Cytochrome c iso-2 OS = Saccharomyces cerevisiae GN = CYC7 PE-1
CYC7_YEAST
12,532.80
47
0


SV = 1






ATP-dependent permease PDR15 OS = Saccharomyces cerevisiae
PDR15_YEAST
172,261.80
47
0


GN = PDR15 PE = 1 SV = 1






60S ribosomal protein L28 OS = Saccharomyces cerevisiae GN = RPL28
RL28_YEAST
16,722.90
46
0


PE = 1 SV = 2






Methionyl-tRNA synthetase, cytoplasmic OS = Saccharomyces
SYMC_YEAST
85,680.90
46
0


cerevisiae GN = MES1 PE = 1 SV = 4






Eukaryotic translation initiation factor 3 subunit G OS = Saccharomyces
EIF3G_YEAST
30,501.60
45
0


cerevisiae GN = TIF35 PE = 1 SV = 1






General transcriptional corepressor TUP1 OS = Saccharomyces
TUP1_YEAST
78,307.20
45
0


cerevisiae GN = TUP1 PE = 1 SV-2






Heat shock protein 42 OS = Saccharomyces cerevisiae GN = HSP42
HSP42_YEAST
42,817.50
44
0


PE = 1 SV = 1






60S ribosomal protein L15-B OS = Saccharomyces cerevisiae
RL15B_YEAST
24,422.60
84
1


GN = RPL158 PE = 1 SV = 2






40S ribosomal protein S23 OS = Saccharomyces cerevisiae
RS23_YEAST
16,038.30
42
0


GN = RPS23A PE = 1 SV = 1






T-complex protein 1 subunit theta OS = Saccharomyces cerevisiae
TCPQ_YEAST
61,663.60
42
0


GN = CCT8 PE = 1 SV = 1






26S protease regulatory subunit 8 homolog OS = Saccharomyces
PRS8_YEAST
45,272.60
41
0


cerevisiae GN = RPT6 PE = 1 SV = 4






SDO1-like protein YHR087W OS = Saccharomyces cerevisiae
SDO1L_YEAST
12,009.80
41
0


GN = YHR087W PE = 1 SV = 1






Mitochondrial escape protein 2 OS = Saccharomyces cerevisiae
YME2_YEAST
96,692.20
40
0


GN = YME2 PE = 1 SV = 1






Alpha-soluble NSF attachment protein SEC63 OS = Saccharomyces cerevisiae
SEC17_YEAST
32,804.40
40
0


GN = SEC17 PE = 1 SV = 4






Protein translocation protein SEC63 OS = Saccharomyces cerevisiae
SEC63_YEAST
75,348.10
40
0


GN = SEC63 PE = 1 SV = 2






Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
PUT2_YEAST
64,437.50
40
0


OS = Saccharomyces cerevisiae GN = PUT2 PE = 1 SV = 2






Polyamine N-acetyltransferase 1 OS = Saccharomyces cerevisiae
PAA1_YEAST
21,948.70
79
1


GN = PAA1 PE = 1 SV = 1






40S ribosomal protein S22-B OS = Saccharomyces cerevisiae
RS22B_YEAST
14,626.50
79
1


GN = RPS22B PE = 1 SV = 3






Phosphoinositide phosphatase SAC1 OS = Saccharomyces cerevisiae
SAC1_YEAST
71,125.90
38
0


GN = SAC1 PE = 1 SV = 1






40S ribosomal protein S26-A OS = Saccharomyces cerevisiae
RS26A_YEAST
13,505.00
38
0


GN = RPS26A PE = 1 SV = 1






26S proteasome regulatory subunit RPN2 OS = Saccharomyces
RPN2_YEAST
104,237.00
76
1


cerevisiae GN = RPN2 PE = 1 SV = 4






Translational activator GCN1 OS = Saccharomyces cerevisiae
GCN1_YEAST
296,710.20
38
0


GN = GCN1 PE = 1 SV = 1






Dolichyl-diphosphooligosaccharide--protein glycosyltransferase
STT3_YEAST
81,532.90
38
0


subunit STT3 OS = Saccharomyces cerevisiae GN = STT3 PE = 1 SV = 2






1,3-beta-glucanosyltransferase GAS5 OS = Saccharomyces cerevisiae
GAS5_YEAST
51,870.70
38
0


GN = GAS5 PE = 1 SV = 1






Acyl-CoA-binding protein OS = Saccharomyces cerevisiae GN = ACB1
ACBP_YEAST
10,061.80
38
0


PE = 1 SV = 3






Tricalbin-1 OS = Saccharomyces cerevisiae GN = TCB1 PE = 1 SV = 1
TCB1_YEAST
133,581.30
37
0


NADP-specific glutamate dehydrogenase 2 OS = Saccharomyces
DHE5_YEAST
49,627.60
37
0


cerevisiae GN = GDH3 PE = 1 SV = 1






Dolichyl-phosphate-mannose--protein mannosyltransferase 1
PMT1_YEAST
92,678.00
37
0


OS = Saccharomyces cerevisiae GN = PMT1 PE = 1 SV = 1






Mitochondrial import inner membrane translocase subunit TIM10
TIM10_YEAST
10,304.60
37
0


OS = Saccharomyces cerevisiae GN = MRS11 PE = 1 SV = 1






Ornithine carbamoyltransferase OS = Saccharomyces cerevisiae
OTC_YEAST
37,846.40
37
0


GN = ARG3 PE = 1 SV = 1






Putative magnesium-dependent phosphatase YER134C
MGDP1_YEAST
20,442.40
36
0


OS = Saccharomyces cerevisiae GN = YER134C PE = 1 SV = 1






Eukaryotic translation initiation factor 4B OS = Saccharomyces
IF4B_YEAST
48,522.50
36
0


cerevisiae GN = TIF3 PE = 1 SV = 1






Mitochondrial escape protein 2 OS = Saccharomyces cerevisiae (strain
YME2_YEAS7
96,662.30
36
0


YJM789) GN = YME2 PE = 3 SV = 1






Vesicle-associated membrane protein-associated protein SCS2
SCS2_YEAST
26,924.80
36
0


OS = Saccharomyces cerevisiae GN = SCS2 PE = 1 SV = 3






Importin beta SMX1 OS = Saccharomyces cerevisiae GN = SXM1 PE = 1
SXM1_YEAST
108,410.90
36
0


SV = 1






Inorganic phosphate transport protein PHO88 OS = Saccharomyces
PHO88_YEAST
21,138.00
36
0


cerevisiae GN = PHO88 PE = 1 SV = 1






Transcription elongation factor SPT6 OS = Saccharomyces cerevisiae
SPT6_YEAST
168,298.50
71
1


GN = SPT6 PE = 1 SV = 2






T-complex protein 1 subunit delta OS = Saccharomyces cerevisiae
TCPD_YEAST
57,605.60
35
0


GN = CCT4 PE = 1 SV = 2






5′-3′ exoribonuclease 1 OS = Saccharomyces cerevisiae GN = KEM1
XRN1_YEAST
175,468.00
70
1


PE = 1 SV = 1






Fumarate reductase OS = Saccharomyces cerevisiae GN = YEL047C
FRDS_YEAST
50,845.00
35
0


PE = 1 SV = 1






3-hydroxy-3-methylgutaryl-coenzyme A reductase 1
HMDH1_YEAST
115,629.10
34
0


OS = Saccharomyces cerevisiae GN = HMG1 PE = 1 SV = 1






26S proteasome regulatory subunit RPN9 OS = Saccharomyces
RPN9_YEAST
45,785.80
34
0


cerevisiae GN = RPN9 PE = 1 SV = 1






Dolichyl-phosphate-mannose--protein mannosyltransferase 2
PMT2_YEAST
86,872.80
34
0


OS = Saccharomyces cerevisiae GN = PMT2 PE = 1 SV = 2






Bifunctional protein GAL10 OS = Saccharomyces cerevisiae
GAL10_YEAST
78,197.30
939
14


GN = GAL10 PE = 1 SV = 2






ATP-dependent bile acid permease OS = Saccharomyces cerevisiae
YBT1_YEAST
189,172.20
33
0


GN = YBT1 PE = 1 SV = 2






Saccharopine dehydrogenase [NAD+, L-lysine-forming]
LYS1_YEAST
41,466.20
33
0


OS = Saccharomyces cerevisiae GN = LYS1 PE = 1 SV = 3






Coatomer subunit gamma OS = Saccharomyces cerevisiae GN = SEC21
COPG_YEAST
104,836.20
32
0


PE = 1 SV = 2






Cell division control protein 53 OS = Saccharomyces cerevisiae
CDC53_YEAST
93,949.60
32
0


GN = CDC53 PE = 1 SV = 1






Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitrochondrial
NDI1_YEAST
57,252.80
32
0


OS = Saccharomyces cerevisiae GN = NDI1 PE = 1 SV = 1






Argininosuccinate lyase OS = Saccharomyces cerevisiae GN = ARG4
ARLY_YEAST
51,991.40
32
0


PE = 1 SV = 2






Zinc finger protein GIS2 OS = Saccharomyces cerevisiae GN = GIS2
GIS2_YEAST
17,102.60
31 
0


PE = 1 SV = 1






Protein kinase MCK1 OS = Saccharomyces cerevisiae GN = MCK1
MCK1_YEAST
43,137.90
31
0


PE = 1 SV = 1






Malate dehydrogenase, peroxisomal OS = Saccharomyces cerevisiae
MDHP_YEAST
37,187.20
31
0


GN = MDH3 PE = 1 SV = 3






T-complex protein 1 subunit zeta OS = Saccharomyces cerevisiae
TCPZ_YEAST
59,925.90
31
0


GN = CCT6 PE = 1 SV = 1






ATP-dependent RNA helicase DBP2 OS = Saccharomyces cerevisiae
DBP2_YEAST
61,001.20
30
0


GN = DBP2 PE = 1 SV = 1






Cytochrome B pre-mRNA-processing protein 6 OS = Saccharomyces
CBP6_YEAST
18,679.70
30
0


cerevisiae GN = CBP6 PE = 1 SV = 1






Protein DCS2 OS = Saccharomyces cerevisiae GN = DCS2 PE = 1 SV = 3
DCS2_YEAST
40,941.80
30
0


Eukaryotic translation initiation factor 3 subunit A OS = Saccharomyces
EIF3A_YEAST
110,348.50
176
3


cerevisiae GN = TIF32 PE = 1 SV = 1






Glucose-signaling factor 2 OS = Saccharomyces cerevisiae GN = GSF2
GSF2_YEAST
45,872.50
58
1


PE = 1 SV = 1






Glycerol-3-phosphate dehydrogenase [NAD+] 2, mitochondrial
GPD2_YEAST
49,422.10
29
0


OS = Saccharomyces cerevisiae GN = GPD2 PE = 1 SV = 2






Prohibitin-2 OS = Saccharomyces cerevisiae GN = PHB2 PE = 1 SV = 2
PHB2_YEAST
34,407.20
29
0


40S ribosomal protein S29-A OS = Saccharomyces cerevisiae
RS29A_YEAST
6,660.70
29
0


GN = RPS29A PE = 1 SV = 3






DNA-directed RNA polymerase I subunit RPA1 OS = Saccharomyces
RPA1_YEAST
186,435.30
29
0


cerevisiae GN = RPA1 PE = 1 SV = 2






Protein transport protein SEC24 OS = Saccharomyces cerevisiae
SEC24_YEAST
103,638.70
29
0


GN = SEC24 PE = 1 SV = 1






Carboxypeptidase Y OS = Saccharomyces cerevisiae GN = PRC1 PE = 1
CBPY_YEAST
59,803.60
28
0


SV = 1






V-type proton ATPase subunit d OS = Saccharomyces cerevisiae
VAOD_YEAST
39,792.40
28
0


GN = VMA6 PE = 1 SV = 2






Uncharacterized protein YJL171C OS = Saccharomyces cerevisiae
YJR1_YEAST
43,014.50
28
0


GN = YJL171C PE = 1 SV = 1






Vacuolar protein sorting/targeting protein PEP1 OS = Saccharomyces
PEP1_YEAST
177,783.50
28
0


cerevisiae GN = PEP1 PE = 1 SV = 1






FACT complex subunit POB3 OS = Saccharomyces cerevisiae
POB3_YEAST
62,995.20
28
0


GN = POB3 PE = 1 SV = 1






Uncharacterized mitochondrial membrane protein FMP10
FMP10_YEAST
27,698.90
28
0


OS = Saccharomyces cerevisiae GN = FMP10 PE = 1 SV = 1






RNA annealing protein YRA1 OS = Saccharomyces cerevisiae
YRA1_YEAST
24,956.30
27
0


GN = YRA1 PE = 1 SV = 2






Mitochondrial outer membrane protein OM45 OS = Saccharomyces
OM45_YEAST
44,582.00
27
0


cerevisiae GN = OM45 PE = 1 SV = 2






Mitochondrial import receptor subunit TOM5 OS = Saccharomyces
TOM5_YEAST
5,984.70
27
0


cerevisiae GN = TOM5 PE = 1 SV = 1






T-complex protein 1 subunit alphs OS = Saccharomyces cerevisiae
TCPA_YEAST
60,482.30
27
0


GN = TCP1 PE = 1 SV = 2






Eukaryotic translation initiation factor 1A OS = Saccharomyces
IF1A_YEAST
17,435.70
26
0


cerevisiae GN = TIF11 PE = 1 SV = 1






Protein MSN5 OS = Saccharomyces cerevisiae GN = MSN5 PE = 1 SV = 1
MSN5_YEAST
142,126.30
26
0


Putative fatty aldehyde dehydrogenase HFD1 OS = Saccharomyces
HFD1_YEAST
59,981.90
26
0


cerevisiae GN = HFD1 PE = 1 SV = 1






Ergosterol biosynthetic protein 28 OS = Saccharomyces cerevisiae
ERG28_YEAST
17,135.80
26
0


GN = ERG28 PE = 1 SV = 1






Protein YRO2 OS = Saccharomyces cerevisiae GN = YRO2 PE = 1 SV = 1
YRO2_YEAST
38,721.30
26
0


Methylene-fatty-acyl-phospholipid synthase OS = Saccharomyces
PEM2_YEAST
23,151.10
26
0


cerevisiae GN = PEM2 PE = 1 SV = 1






Protein MKT1 OS = Saccharomyces cerevisiae GN = MKT1 PE = 1 SV = 2
MKT1_YEAST
94,499.40
25
0


Protein MRH1 OS = Saccharomyces cerevisiae GN = MRH1 PE = 1 SV = 1
MRH1_YEAST
36,192.40
25
0


Eukaryotic translation initiation factor 2 subunit beta
IF2B_YEAST
31,575.70
25
0


OS = Saccharomyces cerevisiae GN = SUI3 PE = 1 SV = 2






Peroxiredoxin TSA2 OS = Saccharomyces cerevisiae GN = TSA2 PE = 1
TSA2_YEAST
21,615.40
24
0


SV = 3






Endoplasmic reticulum vesicle protein 25 OS = Saccharomyces
TMEDA_YEAST
24,106.40
24
0


cerevisiae GN = ERV25 PE = 1 SV = 1






PKHD-type hydroxylase TPA1 OS = Saccharomyces cerevisiae
TPA1_YEAST
74,044.60
24
0


GN = TPA1 PE = 1 SV = 1






SED5-binding protein 3 OS = Saccharomyces cerevisiae GN = SFB3
SFB3_YEAST
103,953.30
24
0


PE = 1 SV = 1






D-lactate dehydrogenase [cytochrome] 3 OS = Saccharomyces
DLD3_YEAST
55,226.80
24
0


cerevisiae GN = DLD3 PE = 1 SV = 1






Single-stranded nucleic acid-binding protein OS = Saccharomyces
SSBP1_YEAST
32,989.90
47
1


cerevisiae GN = DLD3 PE = 1 SV = 1






Protein CWH43 OS = Saccharomyces cerevisiae GN = CWH43 PE = 1
CWH43_YEAST
107,887.70
23
0


SV = 2






T-complex protein 1 subunit eta OS = Saccharomyces cerevisiae
TCPH_YEAST
59,737.10
23
0


GN = CCT7 PE = 1 SV = 1






26S protease regulatory subunit 6B homolog OS = Saccharomyces
PRS6B_YEAST
47,971.50
23
0


cerevisiae GN = RPT3 PE = 1 SV = 1






NADH-cytochrome b5 reductase 1 OS = Saccharomyces cerevisiae
NCB5R_YEAST
31,494.80
23
0


GN = CBR1 PE = 1 SV = 2






Glycogen debranching enzyme OS = Saccharomyces cerevisiae
GDE_YEAST
174,978.70
46
1


GN = GDB1 PE = 1 SV = 1






C-5 sterol desaturase OS = Saccharomyces cerevisiae GN = ERG3
ERG3_YEAST
42,731.70
23
0


PE = 1 SV = 1






13 kDa ribonucleoprotein-associated protein OS = Saccharomyces
SNU13_YEAST
13,569.40
23
0


cerevisiae GN = SNU13 PE = 1 SV = 1






UPF0202 protein KRE33 OS = Saccharomyces cerevisiae GN = KRE33
KRE33_YEAST
119,353.80
23
0


PE = 1 SV = 1






Protein phosphatase PP2A regulatory subunit A OS = Saccharomyces
2AAA_YEAST
79,954.70
23
0


cerevisiae GN = TPD3 PE = 1 SV = 2






Eukaryotic translation initiation factor 2 subunit gamma
IF2G_YEAST
57,857.20
23
0


OS = Saccharomyces cerevisiae GN = GCD11 PE = 1 SV = 1






Midasin OS = Saccharomyces cerevisiae GN = MDN1 PE = 1 SV = 1
MDN1_YEAST
559,323.50
23
0


Galactose-1-phosphate uridyltransferase OS = Saccharomyces
GAL7_YEAST
42,386.00
459
10


cerevisiae GN = GAL7 PE = 1 SV = 4






UPF0121 membrane protein YLL023C OS = Saccharomyces cerevisiae
YL023_YEAST
32,187.70
22
0


GN = YLL0232C PE = 1 SV = 1






Phosphatidylinositol transfer protein PDR16 OS = Saccharomyces
PDR16_YEAST
40,715.80
22
0


cerevisiae GN = PDR16 PE = 1 SV = 1






60S ribosomal protein L43 OS = Saccharomyces cerevisiae
RL43_YEAST
10,090.80
22
0


GN = RPL43A PE = 1 SV = 2






Arginine biosynthesis bifunctional protein ARG7, mitochondrial
ARGJ_YEAST
47,850.20
22
0


OS = Saccharomyces cerevisiae GN = ARG7 PE = 1 SV = 1






Probable family 17 glucosidase SCW4 OS = Saccharomyces cerevisiae
SCW4_YEAST
40,172.20
22
0


GN = SCW4 PE = 1 SV = 1






26S protease subunit RPT4 OS = Saccharomyces cerevisiae
PRS10_YEAST
49,410.10
22
0


GN = RPT4 PE = 1 SV = 4






60S ribosomal protein L3OS = Saccharomyces cerevisiae GN = RPL3
RL3_YEAST
43,757.90
219
5


PE = 1 SV = 4






Phosphoglucomutase-2 OS = Saccharomyces cerevisiae GN = PGM2
PGM2_YEAST
63,091.20
345
8


PE = 1 SV = 1






Uncharacterized phosphatase YNL010W OS = Saccharomyces
YNB0_YEAST
27,481.40
43
1


cerevisiae GN = YNL010W PE = 1 SV = 1






Elongation factor 3A OS = Saccharomyces cerevisiae GN = YEF3 PE = 1
EF3A_YEAST
115,996.20
892
21


SV = 3






Casein kinase II subunit alpha′ OS = Saccharomyces cerevisiae
CSK22_YEAST
39,405.00
21
0


GN = CKA2 PE = 1 SV = 2






54S ribosomal protein L12, mitochondrial OS = Saccharomyces
MNP1_YEAST
20,650.80
21
0


cerevisiae GN = MNP1 PE = 1 SV = 1






Nuclear protein SNF4 OS = Saccharomyces cerevisiae GN = SNF4
SNF4_YEAST
36,402.50
21
0


PE = 1 SV = 1






Eukaryotic initiation factor 4F subunit p150 OS = Saccharomyces
IF4F1_YEAST
107,103.80
21
0


cerevisiae GN = TIF4631 PE = 1 SV = 2






Medium-chain fatty acid ethyl ester synthase/esterase 2
MCFS2_YEAST
51,256.90
21
0


OS = Saccharomyces cerevisiae GN = EHT1 PE = 1 SV = 1






ABC transporter ATP-binding protein ARB1 OS = Saccharomyces
ARB1_YEAST
68,379.50
21
0


cerevisiae GN = ARB1 PE = 1 SV = 1






Cysteinyl-tRNA synthetase OS = Saccharomyces cerevisiae
SYC_YEAST
87,533.90
21
0


GN = YNL247W PE = 1 SV = 1






Protein TTP1 OS = Saccharomyces cerevisiae GN = TTP1 PE = 1 SV = 1
TTP1_YEAST
67,777.60
21
0


26S proteasome regulatory subunit RPN8 OS = Saccharomyces
RPN8_YEAST
38,313.90
21
0


cerevisiae GN = RPN8 PE = 1 SV = 3






NADH-cytochrome b5 reductase 1 OS = Saccharomyces cerevisiae
NCB5R_YEAS7
31,422.60
21
0


(strain YJM789) GN = CBR1 PE = 2 SV = 2






ER membrane protein complex subunit 1 OS = Saccharomyces
EMC1_YEAST
87,185.00
21
0


cerevisiae GN = EMC1 PE = 1 SV = 1






Heat shock protein 78, mitochondrial OS = Saccharomyces cerevisiae
HSP78_YEAST
91,340.80
292
7


GN = HSP78 PE = 1 SV = 2






Nuclear protein STH1/NPS1 OS = Saccharomyces cerevisiae
STH1_YEAST
156,750.60
20
0


GN = STH1 PE = 1 SV = 1






mRNA-binding protein PUF3 OS = Saccharomyces cerevisiae
PUF3_YEAST
98,070.00
20
0


GN = PUF3 PE = 1 SV = 1






Actin-interacting protein 1 OS = Saccharomyces cerevisiae GN = AIP1
AIP1_YEAST
67,326.00
20
0


PE = 1 SV = 1






Cytochrome c iso-1 OS = Saccharomyces cerevisiae GN = CYC1 PE = 1
CYC1_YEAST
12,182.50
80
2


SV = 2






CTP synthase 1 OS = Saccharomyces cerevisiae GN = URA7 PE = 1
URA7_YEAST
64,711.50
20
0


SV = 2






Squalene monooxygenase OS = Saccharomyces cerevisiae GN = ERG1
ERG1_YEAST
55,127.20
20
0


PE = 1 SV = 2






Putative aldehyde dehydrogenase-like protein YHR039C
MSC7_YEAST
71,322.60
20
0


OS = Saccharomyces cerevisiae GN = MSC7 PE = 1 SV = 1






Glucosamine-fructose-6-phosphate aminotransferase [isomerizing]
GFA1_YEAST
80,048.70
78
2


OS = Saccharomyces cerevisiae GN = GFA1 PE = 1 SV = 4






Uncharacterized GTP-binding protein OLA1 OS = Saccharomyces
OLA1_YEAST
44,175.90
155
4


cerevisiae GN = OLA1 PE = 1 SV = 1






Probable 1-acyl-sn-glycerol-3-phosphate acyltransferase
PLSC_YEAST
33,887.80
19
0


OS = Saccharomyces cerevisiae GN = SLC1 PE = 1 SV = 1






Sporulation-specific protein 21 OS = Saccharomyces cerevisiae
MPC70_YEAST
69,881.80
19
0


GN = SPO21 PE = 1 SV = 1






Cell division control protein 42 OS = Saccharomyces cerevisiae
CDC42_YEAST
21,322.60
19
0


GN = CDC42 PE = 1 SV = 2






Serine/threonine-protein phosphatase PP-Z2 OS = Saccharomyces
PPZ2_YEAST
78,494.20
19
0


cerevisiae GN = PPZ2 PE = 1 SV = 4






Putative mitochondrial carrier protein YHM1/SHM1
YHM1_YEAST
33,217.70
19
0


OS = Saccharomyces cerevisiae GN = YHM1 PE = 1 SV = 1






60S ribosomal protein L24-A OS = Saccharomyces cerevisiae
RL24A_YEAST
17,614.40
38
1


GN = RPL24A PE = 1 SV = 1






60S ribosomal protein L35 OS = Saccharomyces cerevisiae
RL35_YEAST
13,910.20
38
1


GN = RPL35A PE = 1 SV = 1






Mitochondrial respiratory chain complexes assembly protein RCA1
RCA1_YEAST
93,280.10
19
0


OS = Saccharomyces cerevisiae GN = RCA1 PE = 1 SV = 1






Prohibitin-1 OS = Saccharomyces cerevisiae GN = PHB1 PE = 1 SV = 2
PHB1_YEAST
31,427.90
38
1


T-complex protein 1 subunit epsilon OS = Saccharomyces cerevisiae
TCPE_YEAST
61,916.50
19
0


GN = CCT5 PE = 1 SV = 3






Translation machinery-associated protein 22 OS = Saccharomyces
DENR_YEAS7
22,495.70
19
0


cerevisiae (strain YJM789) GN = TMA22 PE = 3 SV = 1
(+1)





DnaJ homolog 1, mitochondrial OS = Saccharomyces cerevisiae
MDJ1_YEAST
55,562.00
19
0


GN = MDJ1 PE = 1 SV = 1






Alpha, alpha-trehalose-phosphate synthase [UDP-forming] 56 kDa
TPS1_YEAST
56,148.30
76
2


subunit OS = Saccharomyces cerevisiae GN = TPS1 PE = 1 SV = 2






Acetyl-coenzyme A synthetase 2 OS = Saccharomyces cerevisiae
ACS2_YEAST
75,492.20
228
6


GN = ACS2 PE = 1 SV = 1






60S ribosomal protein L24-B OS = Saccharomyces cerevisiae
RL24B_YEAST
17,548.10
38
1


GN = RPL24B PE = 1 SB = 1






Protein YGP1 OS = Saccharomyces cerevisiae GN = YGP1 PE = 1 SV = 2
YGP1_YEAST
37,328.10
19
0


Actin-related protein 2/3 complex subunit 3 OS = Saccharomyces
ARPC3_YEAST
20,579.60
19
0


cerevisiae GN = ARC18 PE = 1 SV = 1






Isoleucyl-tRNA synthetase, cytoplasmic OS = Saccharomyces
SYIC_YEAST
122,988.30
262
7


cerevisiae GN = ILS1 PE = 1 SV = 1






Eukaryotic translation initiation factor 3 subunit I OS = Saccharomyces
EIF3I_YEAS7
38,756.20
37
1


cerevisiae (strain YJM789) GN = TIF34 PE = 3 SV = 1
(+1)





Dolichol-phosphate mannosyltransferase OS = Saccharomyces
DPM1_YEAST
30,363.40
73
2


cerevisiae GN = DPM1 PE = 1 SV = 3






40S ribosomal protein S29-B OS = Saccharomyces cerevisiae
RS29B_YEAST
6,727.60
18
0


GN = RPS29B PE = 1 SV = 3






Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
PRP43_YEAST
87,564.80
18
0


OS = Saccharomyces cerevisiae GN = PRP43 PE = 1 SV = 1






Translocation protein SEC72 OS = Saccharomyces cerevisiae
SEC72_YEAST
21,608.40
18
0


GN = SEC72 PE = 1 SV = 3






Transcription elongation factor SPT5 OS = Saccharomyces cerevisiae
SPT5_YEAST
115,651.40
36
1


GN = SPT5 PE = 1 SV = 1






Endoplasmic reticulum transmembrane protein 1 OS = Saccharomyces
YET1_YEAST
23,428.60
18
0


cerevisiae GN = YET1 PE = 1 SV = 1






Ferrochelatase, mitochondrial OS = Saccharomyces cerevisiae
HEMH_YEAST
44,597.70
18
0


GN = HEM15 PE = 1 SV = 1






Protein CBP3, mitochondrial OS = Saccharomyces cerevisiae
CBP3_YEAST
39,085.40
18
0


GN = CBP3 PE = 1 SV = 1






Putative protein disulfide-isomerase YIL005W OS = Saccharomyces
YIA5_YEAST
81,223.80
18
0


cerevisiae GN = YIL005W PE = 1 SV = 1






Mitochondrial protein import protein MA65 OS = Saccharomyces
MAS5_YEAST
44,671.70
72
2


cerevisiae GN = YDJ1 PE = 1 SV = 1






Peroxisomal-coenzyme A synthetase OS = Saccharomyces cerevisiae
FAT2_YEAST
60,489.90
18
0


GN = FAT2 PE = 1 SV = 1






Nuclear cap-binding protein complex subunit 1 OS = Saccharomyces
NCBP1_YEAST
100,023.30
36
1


cerevisiae GN = STO1 PE = 1 SV = 2






Proteasome component Y13 OS = Saccharomyces cerevisiae
PSA4_YEAST
28,715.80
18
0


GN = PRE9 PE = 1 SV = 1






Trehalose synthase complex regulatory subunit TSL1
TSL1_YEAST
123,021.70
70
2


OS = Saccharomyces cerevisiae GN = TSL1 PE = 1 SV = 1






Ribosomal RNA-processing protein 12 OS = Saccharomyces cerevisiae
RRP12_YEAST
137,515.10
17
0


GN = RRP12 PE = SV = 1






U3 small nucleolar RNA-associated protein 22 OS = Saccharomyces
UTP22_YEAST
140,492.90
17
0


cerevisiae GN = UTP22 PE = 1 SV = 1






40S ribosomal protein S26-B OS = Saccharomyces cerevisiae
RS26B_YEAST
13,447.00
34
1


GN = RPS26B PE = 1 SV = 1






Elongator complex protein 1 OS = Saccharomyces cerevisiae GN = IKI3
ELP1_YEAST
152,994.20
17
0


PE = 1 SV = 1






Probable 1,3-beta-glucanosyltransferase GAS3 OS = Saccharomyces
GAS3_YEAST
56,796.00
17
0


cerevisiae GN = GAS3 PE = 1 SV = 1






Dynamin-related protein DNM1 OS = Saccharomyces cerevisiae
DNM1_YEAST
84,976.60
68
2


GN = DNM1 PE = 1 SV = 1






Pyruvate dehydrogenase complex protein X component, mitochondrial
ODPX_YEAST
45,363.80
34
1


OS = Saccharomyces cerevisiae GN = PDX1 PE = 1 SV = 1






GTP-binding protein RHO3 OS = Saccharomyces cerevisiae GN = RHO3
RHO3_YEAST
25,312.80
17
0


PE = 1 SV = 2






DNA-directed RNA polymerase I subunit RPA2 OS = Saccharomyces
RPA2_YEAST
135,745.40
33
1


cerevisiae GN = RPA2 PE = 1 SV = 1






54S ribosomal protein YmL6, mitochondrial OS = Saccharomyces
RL4P_YEAST
31,970.50
16
0


cerevisiae GN = YML6 PE = 1 SV = 1






ER-derived vesicles protein ERV29 OS = Saccharomyces cerevisiae
ERV29_YEAST
35,014.90
16
0


GN = ERV29 PE = 1 SV = 1






54S ribosomal protein L3, mitochondrial OS = Saccharomyces
RM03_YEAST
44,001.20
16
0


cerevisiae GN = MRPL3 PE = 1 SV = 2






Pyrroline-5-carboxylate reductase OS = Saccharomyces cerevisiae
P5CR_YEAST
30,131.40
16
0


GN = PRO3 PE = 1 SV = 1






60S ribosomal protein L34-A PS = Saccharomyces cerevisiae
RL34A_YEAST
13,639.20
16
0


GN = RPL34A PE = 1 SV = 1
(+1)





Serine/threonin-protein kinase YPK1 OS = Saccharomyces cerevisiae
YPK1_YEAST
76,483.80
16
0


GN = YPK1 PE = 1 SV = 2






60S ribosomal protein L19 OS = Saccharomyces cerevisiae
RL19_YEAST
21,704.60
32
1


GN = RPL19A PE = 1 SV = 5






CDP-diacylglycerol-inositol 3-phosphatidyltransferase
PIS_YEAST
24,824.30
16
0


OS = Saccharomyces cerevisiae GN = PIS1 PE = 1 SV = 1






60S ribosome subunit biogenesis protein NIP7OS = Saccharomyces
NIP7_YEAST
20,381.10
16
0


cerevisiae GN = NIP7 PE = 1 SV = 1






Cell division control protein 10 OS = Saccharomyces cerevisiae
CDC10_YEAST
37,026.30
16
0


GN = CDC10 PE = 1 SV = 1






E3 ubiquitin-protein ligase RSP5 OS = Saccharomyces cerevisiae
RSP5_YEAST
91,817.40
16
0


GN = RSP5 PE = 1 SV = 1






Glucan 1,3-beta-glucosidase I/II OS = Saccharomyces cerevisiae
EXG1_YEAST
51,312.30
16
0


GN = EXG1 PE = 1 SV = 1






Eukaryotic translation initiation factor 5A-2 OS = Saccharomyces
IF5A2_YEAST
17,114.60
346
11


cerevisiae GN = HYP2 PE = 1 SV = 3






1,4-alpha-glucan-branching enzyme OS = Saccharomyces cerevisiae
GLGB_YEAST
81,118.50
31
1


GN = GLC3 PE = 1 SV = 2






Polyadenylate-binding protein, cytoplasmic and nuclear
PABP_YEAST
64,345.40
183
6


OS = Saccharomyces cerevisiae GN = PAB1 PE = 1 SV = 4






Protein GCY OS = Saccharomyces cerevisiae GN = GCY1 PE = 1 SV = 1
GCY_YEAST
35,079.90
272
9


Putative thiosulfate sulfurtransferase YOR285W OS = Saccharomyces
YO285_YEAST
15,413.30
30
1


cerevisiae GN = YOR285W PE = 1 SV = 1






DNA topoisomerase 2-associated protein PAT1 OS = Saccharomyces
PAT1_YEAST
88,499.40
15
0


cerevisiae GN = PAT1 PE = 1 SV = 3






CAAX prenyl protease 1 OS = Saccharomyces cerevisiae GN = STE24
STE24_YEAST
52,327.50
15
0


PE = 1 SV = 1






Endoplasmic reticulum transmembrane protein 3 OS = Saccharomyces
YET3_YEAST
22,904.20
15
0


cerevisiae GN = YET3 PE = 1 SV = 1






ATP-dependent RNA helicase DOB1 OS = Saccharomyces cerevisiae
MTR4_YEAST
122,058.70
15
0


GN = MTR4 PE = 1 SV = 1






Translation machinery-associated protein 17 OS = Saccharomyces
TMA17_YEAST
16,771.90
15
0


cerevisiae GN = SNF1 PE = 1 SV = 1






Carbon catabolite-derepressing protein kinase OS = Saccharomyces
SNF1_YEAST
72,047.90
15
0


cerevisiae GN = SNF1 PE = 1 SV = 1






tRNA (cytosine-5-)-methyltransferase NCL1 OS = Saccharomyces
NCL1_YEAST
77,879.60
15
0


cerevisiae GN = NCL1 PE = 1 SV = 1






Protein transport protein SEC61 OS = Saccharomyces cerevisiae
SC61A_YEAST
52,940.20
15
0


GN = SEC61 PE = 1 SV = 1






Calcineurin subunit B OS = Saccharomyces cerevisiae GN = CNB1
CANB_YEAST
19,640.10
15
0


PE = 1 SV = 3






Lysophospholipase 1 OS = Saccharomyces cerevisiae GN = PLB1 PE = 1
PLB1_YEAST
71,670.00
15
0


SV = 2






Proteasome component Y7 OS = Saccharomyces cerevisiae GN = PRE8
PSA2_YEAST
27,163.10
15
0


PE = 1 SV = 1






Metal resistance protein YCF1 OS = Saccharomyces cerevisiae
YCFI_YEAST
171,129.30
15
0


GN = YCF1 PE = 1 SV = 2






Ran GTPase-activating protein 1 OS = Saccharomyces cerevisiae
RNA1_YEAST
45,817.80
15
0


GN = RNA1 PE = SV = 2






L-aminoadipate-semialdehyde dehydrogenase OS = Saccharomyces
LYS2_YEAST
155,350.80
30
1


cerevisiae GN = LYS2 PE = 1 SV = 2






Serine hydroxymethyltransferase, mitochondrial OS = Saccharomyces
GLYM_YEAST
53,688.00
30
1


cerevisiae GN = SHM1 PE = 1 SV = 2






Coatomer subunit slpha OS = Saccharomyces cerevisiae GN = RET1
COPA_YEAST
135,611.20
89
3


PE = 1 SV = 2






40S ribosomal protein S10-B OS = Saccharomyces cerevisiae
RS10B_YEAST
12,738.70
89
3


GN = RPS10B PE = 1 SV = 1






40S ribosomal protein S10-A OS = Saccharomyces cerevisiae
RS10A_YEAST
12,739.70
89
3


GN = RPS10A PE = 1 SV = 1






Tryptophan synthase OS = Saccharomyces cerevisiae GN - TRP5 PE = 1
TRP_YEAST
76,626.60
59
2


SV = 1






Serine/threonine-protein phosphatase PP-1-2 OS = Saccharomyces
PP12_YEAST
35,909.00
58
2


cerevisiae GN = GLC7 PE = 1 SV = 1






Aminopeptidase Y OS = Saccharomyces cerevisiae GN = APE3 PE = 1
APE3_YEAST
60,139.20
29
1


SV = 1






Glycerol-3-phosphate dehydrogenase [NAD+] 1 OS = Saccharomyces
GPD1_YEAST
42,868.60
115
4


cerevisiae GN = GPD1 PE = 1 SV = 4






Valyl-tRNA synthetase, mitochondrial OS = Saccharomyces cerevisiae
SYV_YEAST
125,774.70
172
6


GN = VAS1 PE = 1 SV = 2






Aconitate hydratase, mitochondrial OS = Saccharomyces cerevisiae
ACON_YEAST
85,371.60
688
24


GN = ACO1 PE = 1 SV = 2






Elongation factor Tu, mitochondrial OS = Saccharomyces cerevisiae
EFTU_YEAST
47,972.90
57
2


GN = TUF1 PE = 1 SV = 1






Glycerol-3-phosphate O-actyltransferase 2 OS = Saccharomyces
GPT2_YEAST
83,648.60
14
0


cerevisiae GN = GPT2 PE = 1 SV = 1






Putative ribsomal RNA methyltransferase Nop2 OS = Saccharomyces
NOP2_YEAST
69,814.30
14
0


cerevisiae GN = NOP2 PE = 1 SV = 1






Serine/threonine-protein kinase YPK2/YKR2 OS = Saccharomyces
YPK2_YEAST
76,669.00
14
0


cerevisiae GN = YPK2 PE = 1 SV = 1






Xanthine phosphoribosyltransferase 1 OS = Saccharomyces cerevisiae
XPT1_YEAST
23,672.00
14
0


GN = XPT1 PE = 1 SV = 1






3-hydroxy-3-methylglutaryl-coenzyme A reductase 2
HMDH2_YEAST
115,696.90
14
0


OS = Saccharomyces cerevisiae GN = HMG2 PE = 1 SV = 1






3-keto-steroid reductase OS = Saccharomyces cerevisiae GN = ERG27
ERG27_YEAST
39,726.60
14
0


PE = 1 SV = 1






Ras-like protein 2 OS = Saccharomyces cerevisiae GN = RAS2 PE = 1
RAS2_YEAST
34,705.00
14
0


SV = 4






Protein phosphatase 1 regulatory subunit SDS22 OS = Saccharomyces
SDS22_YEAST
38,890.20
14
0


cerevisiae GN = SDS22 PE = 1 SV = 1






Ubiquitin-like protein SMT3 OS = Saccharomyces cerevisiae GN = SMT3
SMT3_YEAST
11,597.50
28
1


PE = 1 SV = 1






Sphingosine-1-phosphate lyase OS = Saccharomyces cerevisiae
SGPL_YEAST
65,567.50
14
0


GN = DPL1 PE = 1 SV = 1






Protein transport protein SSS1 OS = Saccharomyces cerevisiae
SC61G_YEAST
8,943.80
14
0


GN = SSS1 PE = 1 SV = 2






UPF0675 endoplasmic reticulum membrane protein YNR021W
YN8B_YEAST
47,095.10
14
0


OS = Saccharomyces cerevisiae GN = YNR021W PE = 1 SV = 3






Non-classical export protein 2 OS = Saccharomyces cerevisiae
NCE2_YEAST
18,967.70
14
0


GN = NCE102 PE = 1 SV = 1






Reduced viability upon starvation protein 161 OS = Saccharmomyces
RV161_YEAST
30,251.90
14
0


cerevisiae GN = RVS161 PE = 1 SV = 1






Cytochrome b5 OS = Saccharomyces cerevisiae GN = CYB5 PE = 1
CYB5_YEAST
13,297.10
14
0


SV = 2






60S ribosomal protein L37-A OS = Saccharomyces cerevisiae
RL37A_YEAST
9,850.40
14
0


GN = RPL37A PE = 1 SV = 2






Calmodulin OS = Saccharomyces cerevisiae GN = CMD1 PE = 1 SV = 1
CALM_YEAST
16,135.50
14
0


Actin-related protein 2/3 complex subunit 5 OS = Saccharomyces
ARPC5_YEAST
17,134.60
14
0


cerevisiae GN = ARC15 PE = 1 SV = 1






Mitochondrial outer membrane protein SCY_3392
YKR18_YEAS7
81,773.40
14
0


OS = Saccharomyces cerevisiae (strain YJM789) GN = SCY_3392 PE = 3
(+1)





SV = 1






tRNA pseudouridine synthase 1 OS = Saccharomyces cerevisiae
PUS1_YEAST
62,145.30
14
0


GN = PUS1 PE = 1 SV = 1






Heterotrimeric G protein gamma subunit GPG1 OS = Saccharomyces
GPG1_YEAST
14,922.30
14
0


cerevisiae GN = GPG1 PE = 1 SV = 1






Anthranilate synthase component 1 OS = Saccharomyces cerevisiae
TRPE_YEAST
56,769.50
14
0


GN = TRP2 PE = 1 SV = 4






UPF0662 protein YPL260W OS = Saccharomyces cerevisiae
YP260_YEAST
62,782.70
27
1


GN = YPL260W PE = 1 SV = 1






NADPH-dependent 1-acyldihydroxyactone phosphate reductase
AYR1_YEAST
32,815.30
27
1


OS = Saccharomyces cerevisiae GN = AYR1 PE = 1 SV = 1






Long-chain-fatty-acid--CoA ligase 1 OS = Saccharomyces cerevisiae
LCF1_YEAST
77,868.10
81
3


GN = FAA1 PE = 1 SV = 1






Small COPII coat GTPase SAR1 OS = Saccharomyces cerevisiae
SAR1_YEAST
21,451.50
53
2


GN = SAR1 PE = 1 SV = 1






GMP synthase [glutamine-hydrolyzing] OS = Saccharomyces cerevisiae
GUAA_YEAST
58,483.40
53
2


GN = GUA1 PE = 1 SV = 4






Mitochondrial outer membrane protein porin 1 OS = Saccharomyces
VDAC1_YEAST
30,429.50
185
7


cerevisiae GN = POR1 PE = 1 SV = 4






ATP-dependent helicase NAM7 OS = Saccharomyces cerevisiae
NAM7_YEAST
109,432.60
13
0


GN = NAM7 PE = 1 SV = 1






Proteasome component PRE2 OS = Saccharomyces cerevisiae
PSB5_YEAST
31,636.90
13
0


GN = PRE2 PE = 1 SM = 3






Homocitrate synthase, mitochondrial OS = Saccharomyces cerevisiae
HOSM_YEAST
48,595.50
78
3


GN = LYL21 PE = 1 SV = 1






Nucleolar complex protein 2 OS = Saccharomyces cerevisiae
NOC2_YEAST
81,605.10
13
0


GN = NOC2 PE = 1 SV = 2






Transcriptional regulatory protein SIN3 OS = Saccharomyces cerevisiae
SIN3_YEAST
174,843.10
13
0


GN = SIN3 PE = 1 SV = 2






Ribosome biogenesis protein ERB1 OS = Saccharomyces cerevisiae
ERB1_YEAS7
91,706.30
13
0


(strain YJM789) GN = ERB1 PE = 3 SV = 1
(+1)





Dihydroxy-acid dehydratase, mitochondrial OS = Saccharomyces
ILV3_YEAST
62,862.80
78
3


cerevisiae GN = ILV3 PE = 1 SV = 2






Uncharacterized protein YKL054C OS = Saccharomyces cerevisiae
YKF4_YEAST
83,968.30
13
0


GN = YKL054C PE = 1 SV = 1






DNA-directed RNA polymerases I, II, and III subunit RPABC5
RPAB5_YEAST
8,278.00
13
0


OS = Saccharomyces cerevisiae GN = RPB10 PE = 1 SV = 2






Mitochondrial presequence protease OS = Saccharomyces cerevisiae
CYM1_YEAST
112,185.50
26
1


GN = CYM1 PE = 1 SV = 2






Amidophosphoribosyltransferase OS = Saccharomyces cerevisiae
PUR1_YEAST
56,720.30
13
0


GN = ADE4 PE = 1 SV = 2






Protein ERP1 OS = Saccharomyces cerevisiae GN = ERP1 PE = 1 SV = 1
ERP1_YEAST
24,724.00
13
0


Hsp90 co-chaperone HCH1 OS = Saccharomyces cerevisiae
HCH1_YEAST
17,246.80
13
0


GN = HCH1 PE = 1 SV = 1






Acetyl-CoA carboxylase OS = Saccharomyces cerevisiae GN = FAS3
ACAC_YEAST
250,359.50
572
22


PE = 1 SV = 2






Mitochondrial outer membrane protein IML2 OS = Saccharomyces
IML2_YEAS7
82,553.00
13
0


cerevisiae (strain YJM789) GN = IML2 PE = 3 SV = 1
(+1)





Choline-phosphate cytidyltransferase OS = Saccharomyces cerevisiae
PCY1_YEAST
49,408.40
13
0


GN = PCT1 PE = 1 SV = 2






Nucleosome assembly protein OS = Saccharomyces cerevisiae
NAP1_YEAST
47,886.10
13
0


GN = NAP1 PE = 1 SV = 2






THO complex subunit 2 OS = Saccharomyces cerevisiae GN = THO2
THO2_YEAST
183,940.50
13
0


PE = 1 SV = 1






Sec sixty-one protein homolog OS = Saccharomyces cerevisiae
SSH1_YEAST
53,314.50
13
0


GN = SSH1 PE = 1 SV = 1






Cytochrome c heme lyase OS = Saccharomyces cerevisiae GN = CYC3
CCHL_YEAST
30,080.70
13
0


PE = 1 SV = 1






Prefoldin subunit 4 OS = Saccharomyces cerevisiae GN = GIM3 PE = 1
PFD4_YEAST
15,181.00
13
0


SV = 1






Gamma-glutamyl phosphate reductase OS = Saccharomyces
PROA_YEAST
49,742.20
13
0


cerevisiae GN = PRO2 PE = 1 SV = 1






60S ribosomal protein L37-B OS = Saccharomyces cerevisiae
RL37B_YEAST
9,868.30
13
0


GN = RPL378B PE = 1 SV = 2






UPF0368 protein YPL225W OS = Saccharomyces cerevisiae
YP225_YEAST
17,445.20
26
1


GN = YPL225W PE = 1 SV = 1






Dolichyl-phosphate-mannose--protein mannosyltransferase 4
PMT4_YEAST
87,968.60
13
0


OS = Saccharomyces cerevisiae GN = PMT4 PE = 1 SV = 1






Increased sodium tolerance protein 2 OS = Saccharomyces cerevisiae
IST2_YEAST
105,908.10
13
0


GN = IST2 PE = 1 SV = 1






Glucokinase-1 OS = Saccharomyces cerevisiae GN = GLK1 PE = 1 SV = 1
HXKG_YEAST
55,379.10
231
9


Suppressor protein STM1 OS = Saccharomyces cerevisiae GN = STM1
STM1_YEAST
29,995.40
202
8


PE = 1 SV = 3






Uridylate kinase OS = Saccharomyces cerevisiae GN = URA6 PE = 1
UMPK_YEAST
22,933.90
12
0


SV = 1






Myosin light chain 1 OS = Saccharomyces cerevisiae GN = MLC1 PE = 1
MLC1_YEAST
16,445.30
24
1


SV = 1






Glucose-repressible alcohol dehydrogenase transcriptional effector
CCR4_YEAST
94,702.70
12
0


OS = Saccharomyces cerevisiae GN = CCR4 PE = 1 SV = 1






54S ribosomal protein L1, mitochondrial OS = Saccharomyces
RM01_YEAST
30,997.30
12
0


cerevisiae GN = MRPL1 PE = 1 SV = 1






Nuclear polyadenylated RNA-binding protein 3 OS = Saccharomyces
NAB3_YEAST
90,438.50
12
0


cerevisiae GN = NAB3 PE = 1 SV = 1






Phosphoglycerate mutase 2 OS = saccharomyces cerevisiae
PMG2_YEAST
36,074.50
12
0


GN = GPM2 PE = 1 SV = 1






3′(2′),5′-bisphosphate nucleotidase OS = Saccharomyces cerevisiae
HAL2_YEAST
39,150.30
12
0


GN = HAL2 PE = 1 SV = 1






Protein SEY1 OS = Saccharomyces cerevisiae (strain AWRI1631)
SEQY1_YEAS6
89,425.20
12
0


GN = SEY1 PE = 3 SV = 1
(+2)





Thiamine metabolism regulatory protein THI3 OS = Saccharomyces
THI3_YEAST
68,367.90
12
0


cerevisiae GN = THI3 PE = 1 SV = 1






Alpha-mannosidase OS = Saccharomyces cerevisiae GN = AMS1 PE = 1
MAN1_YEAST
124,503.20
24
1


SV = 2






[NU+] prion formation protein 1 OS = Saccharomyces cerevisiae
NEW1_YEAST
134,335.50
12
0


GN = NEW1 PE = 1 SV = 1






T-complex protein 1 subunit beta OS = Saccharomyces cerevisiae
TCPB_YEAST
57,205.70
12
0


GN = CCT2 PE = 1 SV = 1






Putative zinc metalloproteinase YIL108W OS = Saccharomyces
YIK8_YEAST
77,416.50
12
0


cerevisiae GN = YIL108W PE = 1 SV = 1






Prefoldin subunit 5 OS = Saccharomyces cerevisiae GN = GIM5 PE = 1
PFD5_YEAST
18,356.30
12
0


SV = 1






Probable glycosidase CRH2 OS = Saccharomyces cerevisiae
CRH2_YEAST
49,906.20
12
0


GN = UTR2 PE = 1 SV = 3






Coatomer subunit epsilon OS = Saccharomyces cerevisiae GN = SEC28
COPE_YEAST
33,830.60
12
0


PE = 1 SV = 2






26S proteasome regulatory subunit RPN13 OS = Saccharomyces
RPN13_YEAST
17,902.50
12
0


cerevisiae GN = RPN13 PE = 1 SV = 1






40S ribosomal protein S28-A OS = Saccharomyces cerevisiae
RS28A_YEAST
7,591.70
24
1


GN = RPS28A PE = 1 SV = 1






D-3-phosphoglycerate dehydrogenase 1 OS = Saccharomyces
SERA_YEAST
51,194.10
12
0


cerevisiae GN = SER3 PE = 1 SV = 1






Adenylosuccinate synthetase OS = Saccharomyces cerevisiae
PURA_YEAST
48,280.40
12
0


GN = ADE12 PE = 1 SV = 3






CTP synthase 2 OS = Saccharomyces cerevisiae (strain YJM789)
URA8_YEAS7
64,497.40
12
0


GN = URA8 PE = 3 SV = 1
(+1)





ATP-dependent RNA helicase HAS1 OS = Saccharomyces cerevisiae
HAS1_YEAST
56,720.20
12
0


GN = HAS1 PE = 1 SV = 1






Zinc finger protein ZPR1 OS = Saccharomyces cerevisiae GN = ZPR1
ZPR1_YEAST
55,072.70
12
0


PE = 1 SV = 1






26S proteasome regulatory subunit RPN3 OS = Saccharomyces
RPN3_YEAST
60,426.30
12
0


cerevisiae GN = RPN3 PE = 1 SV = 4






Peroxisomal membrane protein PMP27 OS = Saccharomyces
PEX11_YEAST
26,876.20
12
0


cerevisiae GN = PEX11 PE = 1 SV = 2






Ribose-phosphate pyrophosphokinase 5 OS = Saccharomyces
KPR5_YEAST
53,506.20
12
0


cerevisiae GN = PRS5 PE = 1 SV = 1






U6 snRNA-associated Sm-like protein LSm6 OS = Saccharomyces
LSM6_YEAS7
9,398.00
12
0


cereviaiae (strain YJM789) GN = LSM6 PE = 3 SV = 1
(+1)





Protein HMF1 OS = Saccharomyces cerevisiae GN = HMF1 PE = 1 SV = 1
HMF1_YEAST
13,905.90
12
0


General negative regulator of transcription subunit 1
NOT1_YEAST
240,344.80
12
0


OS = Saccharomyces cerevisiae GN = NOT1 PE = 1 SV = 2






Putative glucokinase-2 OS = Saccharomyces cerevisiae GN = EMI2
EMI2_YEAST
55,923.00
92
4


PE = 1 SV = 1






26S protease regulatory subunit 4 homolog OS = Saccharomyces
PRS4_YEAST
48,830.50
23
1


cerevisiae GN = RPT2 PE = 1 SV = 3






Sphingolipid long chain base-responsive protein LSP1
LSP1_YEAST
38,071.60
113
5


OS = Saccharomyces cerevisiae GN = LSP1 PE = 1 SV = 1






UPF0001 protein YBL036C OS = Saccharomyces cerevisiae
YBD6_YEAST
29,l24.20
11
0


GN = YBL036C PE = 1 SV = 1






Galactose/lactose metabolism regulatory protein GAL80
GAL80_YEAST
48,325.40
11
0


OS = Saccharomyces cerevisiae GN = GAL80 PE = 1 SV = 2






U3 small nucleolar ribonucleoprotein protein IMP3
IMP3_YEAST
21,886.10
11
0


OS = Saccharomyces cerevisiae GN = IMP3 PE = 1 SV = 1






U3 small nucleolar RNA-associated protein 21 OS = Saccharomyces
UPT21_YEAST
104,794.60
11
0


cerevisiae GN = UPT21 PE = 1 SV = 1






DNA polymerase alpha catalytic subunit A OS = Saccharomyces
DPOA_YEAST
166,815.30
11
0


cerevisiae GN = POL1 PE = 1 SV = 2






Probable glycerophosphodiester phosphodiesterase YPL206C
YP206_YEAST
37,071.30
11
0


OS = Saccharomyces cerevisiae GN = YPL206C PE = 1 SV = 1






Cytochrome c oxidase assembly protein COX15 OS = Saccharomyces
COX15_YEAST
54,660.50
11
0


cerevisiae GN = COX15 PE = 1 SV = 1






U6 snRNA-associated Sm-like protein LSm5 OS = Saccharomyces
LSM5_YEAST
10,423.20
11
0


cerevisiae GN = LSM5 PE = 1 SV = 1






60S ribosomal protein L29 OS = Saccharomyces cerevisiae GN = RPL29
RL29_YEAST
6,669.10
11
0


PE = 1 SV = 3






Tricalbin-3 OS = Saccharomyces cerevisiae GN = TCB3 PE = 1 SV = 1
TCB3_YEAST
171,081.40
22
1


Peroxiredoxin HYR1 OS = Saccharomyces cerevisiae GN = HYR1 PE = 1
GPX3_YEAST
18,642.20
22
1


SV = 1






Glucose-6-phosphate 1 dehydrogenase OS = Saccharomyces
G6PD_YEAST
57,523.60
44
2


cerevisiae GN = ZWF1 PE = 1 SV = 4






Endosomal protein P24B OS = Saccharomyces cerevisiae GN = EMP24
EMP24_YEAST
23,332.70
11
0


PE = 1 SV = 1






Proteasome component C1 OS = Saccharomyces cerevisiae
PSA3_YEAST
31,536.40
11
0


GN = PRE10 PE = 1 SV = 2






26S proteasome regulatory subunit RPN6 OS = Saccharomyces
RPN6_YEAST
49,776.20
11
0


cerevisiae GN = RPN6 PE = 1 SV = 3






Monothiol glutaredoxin-3 OS = Saccharomyces cerevisiae GN = GRX3
GLRX3_YEAST
32,481.70
11
0


PE = 1 SV = 1






C-8 sterol isomerase OS = Saccharomyces cerevisiae GN = ERG2 PE = 1
ERG2_YEAST
24,896.60
11
0


SV = 1






Uncharacterized membrane glycoprotein YNR065C
YN94_YEAST
125,204.80
11
0


OS = Saccharomyces cerevisiae GN = YNR065C PE = 1 SV = 1






Ubiquitin carboxyl-terminal hydrolase 6 OS = Saccharomyces
UBP6_YEAST
57,112.50
11
0


cerevisiae GN = UBP6 PE = 1 SV = 1






Histone chaperaone ASF1 OS = Saccharomyces cerevisiae GN = ASF1
ASF1_YEAST
31,603.10
11
0


PE = 1 SV = 1






Pumilio homology domain family member 6 OS = Saccharomyces
PUF6_YEAST
75,109.00
22
1


cerevisiae GN = PUF6 PE = 1 SV = 1






Mitochondrial outer membrane protein OM14 OS = Saccharomyces
OM14_YEAS7
14,609.90
11
0


cerevisiae (strain YJM789) GN = OM14 PE = 3 SV = 1
(+1)





AP-1 complex subunit gamma-1 OS = Saccharomyces cerevisiae
AP1G1_YEAST
93,631.50
11
0


GN = APL4 PE = 1 SV = 1






Signal recognition particle subunit SRP72 OS = Saccharomyces
SRP72_YEAST
73,544.80
11
0


cerevisiae GN = SRP72 PE = 1 SV = 2






Protein transport protein SEC31 OS = Saccharomyces cerevisiae
SEC31_YEAST
138,706.80
11
0


GN = SEC31 PE = 1 SV = 2






Phosphatidylethanolamine N-methyltransferase OS = Saccharomyces
PEM1_YEAST
101,208.50
11
0


cerevisiae GN = PEM1 PE = 1 SV = 1






Mitochondrial import inner membrane translocase subunit TIM16
TIM16_YEAST
16,216.50
11
0


OS = Saccharomyces cerevisiae GN = PAM16 PE = 1 SV = 1






Phosphatidate cytidylyltransferase OS = Saccharomyces cerevisiae
CDS1_YEAST
51,825.70
11
0


GN = CDS1 PE = 1 SV = 1






26S proteasome regulatory subunit RPN12 OS = Saccharomyces
RPN12_YEAST
31,922.00
11
0


cerevisiae GN = RPN12 PE = 1 SV = 3






N-terminal acetyltransferase A complex subunit NAT1
NAT1_YEAST
98,912.00
11
0


OS = Saccharomyces cerevisiae GN = NAT1 PE = 1 SV = 2






Nucleolar pre-ribosomal-associated protein 1 OS = Saccharomyces
URB1_YEAST
203,200.10
11
0


cerevisiae GN = URB1 PE = 1 SV = 2






GU4 nucleic-binding protein 1 OS = Saccharomyces cerevisiae
G4P1_YEAST
42,084.50
87
4


GN = ARC1 PE = 1 SV = 2






Mitochondrial peculiar membrane protein 1 OS = Saccharomyces 
MPM1_YEAST
28,471.40
43
2


cerevisiae GN = MPM1 PE = 1 SV = 1






6-phosphogluconate dehydrogenase, decarboxylating 1
6PGD1_YEAST
53,545.30
494
23


OS = Saccharomyces cerevisiae GN = GND1 PE = 1 SV = 1






Transcription-associated protein 1 OS = Saccharomyces cerevisiae
TRA1_YEAST
433,195.70
21
1


GN = TRA1 PE = 1 SV = 1






RNA polymerase-associated protein CTR9 OS = Saccharomyces
CTR9_YEAST
124,663.10
42
2


cerevisiae GN = CTR9 PE = 1 SV = 2






DNA-directed RNA polymerases I, II, and III subunit RPABC3
RPAB3_YEAST
16,512.10
21
1


OS = Saccharomyces cerevisiae GN = RPB8 PE = 1 SV = 1






Ribonucleoside-diphosphate reductase large chain 1
RIR1_YEAST
99,564.50
21
1


OS = Saccharomyces cerevisiae GN = RNR1 PE = 1 SV = 2






60S ribosomal protein L10 OS = Saccharomyces cerevisiae GN = RPL10
RL10_YEAST
25,362.10
168
8


PE = 1 SV = 1






Sphingolipid long chain base-responsive protein PIL1
PIL1_YEAST
38,350.30
166
8


OS = Saccharomyces cerevisiae GN = PIL1 PE = 1 SV = 1






Ribosome-associated complex subunit SSZ1 OS = Saccharomyces
SSZ1_YEAST
58,239.50
145
7


cerevisiae GN = SSZ1 PE = 1 SV = 2






Golgin IMH1 OS = Saccharomyces cerevisiae GN = IMH1 PE = 1 SV = 1
IMH1_YEAST
105,231.40
10
0


Protein SCO2, mitochondrial OS = Saccharomyces cerevisiae
SCO2_YEAST
34,890.60
10
0


GN = SCO2 PE = 1 SV = 1






3-ketoacyl-CoA reductase OS = Saccharomyces cerevisiae GN = IFA38
MKAR_YEAST
38,709.70
10
0


PE = 1 SV = 1






Iron transport multicopper oxidase FET5 OS = Saccharomyces
FET5_YEAST
70,880.90
10
0


cerevisiae GN = FET5 PE = 1 SV = 1






Protein ISD11 OS = Saccharomyces cerevisiae GN = ISD11 PE = 1 SV = 1
ISD11_YEAST
11,266.40
10
0


Mitochondrial distribution and morphology protein 38
MDM38_YEAST
65,008.10
10
0


OS = Saccharomyces cerevisiae GN = MDM38 PE = 1 SV = 1






Elongation of fatty acids protein 3 OS = Saccharomyces cerevisiae
ELO3_YEAST
39,467.00
10
0


GN = ELO3 PE = 1 SV = 1






Nucleolar GTP-binding protein 1 OS = Saccharomyces cerevisiae
NOG1_YEAST
74,412.80
10
0


GN = NOG1 PE = 1 SV = 1






Peptidyl-prolyl cis-trans isomerase ESS1 OS = Saccharomyces
ESS1_YEAST
19,404.90
10
0


cerevisiae GN = ESS1 PE = 1 SV = 3






ATPase GET3 OS = Saccharomyces cerevisiae (strain RM11-1a)
GET3_YEAS1
39,355.10
10
0


GN = GET3 PE = 3 SV = 1
(+2)





Protein APA1 OS = Saccharomyces cerevisiae GN = APA1 PE = 1 SV = 4
APA1_YEAST
36,494.20
10
0


Mitochondrial respiratory chain complexes assembly protein AFG3
AFG3_YEAST
84,547.40
10
0


OS = Saccharomyces cerevisiae GN = AFG3 PE = 1 SV = 1






Calcium-transporting ATPase 2 OS = Saccharomyces cerevisiae
ATC2_YEAST
130,866.40
10
0


GN = PMC1 PE = 1 SV = 1






Probable intramembrane protease YKL100C OS = Saccharomyces
YKK0_YEAST
67,528.20
10
0


cerevisiae GN = YKL100C PE = 1 SV = 1






KH domain-containing protein YBL032W OS = Saccharomyces
YBD2_YEAST
41,684.60
10
0


cerevisiae GN = YBL032W PE = 1 SV = 1






Mitochondrial import receptor subunit TOM22 OS = Saccharomyces
TOM22_YEAST
16,790.90
10
0


cerevisiae GN = TOM22 PE = 1 SV = 3






Protein MSP1 OS = Saccharomyces cerevisiae GN = MSP1 PE = 1 SV = 2
MSP1_YEAST
40,346.50
10
0


UPF0364 protein YMR027W OS = Saccharomyces cerevisiae
YMR7_YEAST
54,130.90
10
0


GN = YMR027W PE = 1 SV = 1






Uncharacterized protein YJL217W OS = Saccharomyces cerevisiae
YJV7_YEAST
21,966.80
10
0


GN = YJL217W PE = 1 SV = 1






ER membrane protein complex subunit 4 OS = Saccharomyces
EMC4_YEAST
21,460.70
10
0


cerevisiae GN = EMC4 PE = 1 SV = 1






Sm-like protein LSm1 OS = Saccharomyces cerevisiae GN = LSM1
LSM1_YEAST
20,307.60
10
0


PE = 1 SV = 1






Probable alpha-1,6-mannosyltransferase MNN10 OS = Saccharomyces
MNN10_YEAST
46,750.50
10
0


cerevisiae GN = MNN10 PE = 1 SV = 1






Protein HAM1 OS = Saccharomyces cerevisiae GN = HAM1 PE = 1 SV = 1
HAM1_YEAST
22,093.90
10
0


NADPH-dependent methylglyoxal reductase GRE2
GRE2_YEAST
38,170.30
10
0


OS = Saccharomyces cerevisiae GN = GRE2 PE = 1 SV = 1






Alpha-1,2-mannosyltransferase KTR1 OS = Saccharomyces cerevisiae
KTR1_YEAST
46,023.70
10
0


GN = KTR1 PE = 1 SV = 1






Protein VTH1 OS = Saccharomyces cerevisiae GN = VTH1 PE = 1 SV = 1
VTH1_YEAST
174,434.90
10
0



(+1)





Trehalose synthase complex regulatory subunit TPS3
TPS3_YEAST
118,837.50
10
0


OS = Saccharomyces cerevisiae GN = TPS3 PE = 1 SV = 3






Heat shock protein 60, mitochondrial OS = Saccharomyces cerevisiae
HSP60_YEAST
60,7553.00
743
38


GN = HSP60 PE = 1 SV = 1






Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
ODPB_YEAST
40,054.20
77
4


OS = Saccharomyces cerevisiae GN = PDB1 PE = 1 SV = 2






Pyruvate dehydrogenase E1 component subunit alpha, mitochondrial
ODPA_YEAST
46,344.40
96
5


OS = Saccharomyces cerevisiae GN = PDA1 PE = 1 SV = 2






Actin-related protein 3 OS = Saccharomyces cerevisiae GN = ARP3
ARP3_YEAST
49,542.70
19
1


PE = 1 SV = 1






AMP deaminase OS = Saccharomyces cerevisiae GN = AMD1 PE = 1
AMPD_YEAST
93,304.30
19
1


SV = 2






Lon protease homolog, mitochondrial OS = Saccharomyces cerevisiae
LONM_YEAST
127,116.80
56
3


GN = PIM1 PE = 1 SV = 2






Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial
IDH1_YEAST
39,325.30
223
12


OS = Saccharomyces cerevisiae GN = IDH1 PE = 1 SV = 2






Serine hydroxymethyltransferase, cytosolic OS = Saccharomyces
GLYC_YEAST
52,219.70
110
6


cerevisiae GN = SHM2 PE = 1 SV = 2






Rab proteins geranylgeranyltransferase component A
RAEP_YEAST
67,374.90
9
0


OS = Saccharomyces cerevisiae GN = MRS6 PE = 1 SV = 2






37S ribosomal protein MRP1, mitochondrial OS = Saccharomyces
RT01_YEAST
36,730.90
9
0


cerevisiae GN = MRP1 PE = 1 SV = 2






Carboxypeptidase S OS = Saccharomyces cerevisiae GN = CPS1 PE = 1
CBPS_YEAST
64,599.30
9
0


SV = 2






Probable glucose transporter HXT5 OS = Saccharomyces cerevisiae
HXT5_YEAST
66,252.90
9
0


GN = HXT5 PE = 1 SV = 1






Glycerol-3-phosphate dehydrogenase, mitochondrial
GPDM_YEAST
72,390.60
90
5


OS = Saccharomyces cerevisiae GN = GUT2 PE = 1 SV = 2






Cytochrome b2, mitochondrial OS = Saccharomyces cerevisiae
CYB2_YEAST
65,541.20
9
0


GN = CYB2 PE = 1 SV = 1






Translation machinery-associated protein 20 OS = Saccharomyces
TMA20_YEAST
20,278.30
9
0


cerevisiae GN = TMA20 PE = 1 SV = 1






D-arabinono-1,4-lactone oxidase OS = Saccharomyces cerevisiae
ALO_YEAST
59,494.80
9
0


GN = ALO1 PE = 1 SV = 1






Protein phosphatase 2C homolog 3 OS = Saccharomyces cerevisiae
PP2C3_YEAST
51,391.60
9
0


GN = PTC3 PE = 1 SV = 3






DNA-directed RNA polymerase II subunit RPB9 OS = Saccharomyces
RPB9_YEAST
14,288.00
9
0


cerevisiae GN = RPB9 PE = 1 SV = 1






Casein kinase II subunit alpha OS = Saccharomyces cerevisiae
CSK21_YEAST
44,669.80
9
0


GN = CKA1 PE = SV = 1






26S protease regulatory subunit 6A OS = Saccharomyces cerevisiae
PRS6A_YEAST
48,257.20
9
0


GN = RPT5 PE ==0 SV = 3






Enoyl reductase TSC13OS = Saccharomyces cerevisiae GN = TSC13
TSC13_YEAST
36,770.00
9
0


PE = 1 SV = 1






H/ACA ribonucleoprotein complex subunit 2 OS = Saccharomyces
NHP2_YEAST
17,122.10
9
0


cerevisiae GN = NHP2 PE = 1 SV = 2






Retrograde regulation protein 2 OS = Saccharomyces cerevisiae
RTG2_YEAST
65,573.60
9
0


GN = RTG2 PE = 1 SV = 2






Uncharacterized protein YDR476C OS = Saccharomyces cerevisiae
YD476_YEAST
25,266.70
9
0


GN = YDR476C PE = 1 SV = 1






DNA-directed RNA polymerases I and III subunit RPAC2
RPAC2_YEAST
16,150.90
9
0


OS = Saccharomyces cerevisiae GN = RPC19 PE = 1 SV = 1






GPI transamidase component GPI16 OS = Saccharomyces cerevisiae
GPI16_YEAST
68,775.10
9
0


GN = GPI16 PE = 1 SV = 2






V-type proton ATPase subunit e OS = Saccharomyces cerevisiae
VA0E_YEAST
8,381.10
9
0


GN = VMA9 PE = 1 SV = 1






Cell division control protein 28 OS = Saccharomyces cerevisiae
CDC28_YEAST
34,063.40
18
1


GN = CDC28 PE = 1 SV = 1






Serine/threonine-protein phosphatase 2B catalytic subunit A2
PP2B2_YEAST
68,529.90
9
0


OS = Saccharomyces cerevisiae GN = CNA2 PE = 1 SV = 2






GTP-binding protein YPT31/YPT8 OS = Saccharomyces cerevisiae
YPT31_YEAST
24,469.90
9
0


GN = YPT31 PE = 1 SV = 3
(+1)





FK506-binding nuclear protein OS = Saccharomyces cerevisiae
FKBP3_YEAST
46,554.20
9
0


GN = FPR3 PE = 1 SV = 2






D-3-phosphoglycerate dehydrogenase 2 OS = Saccharomyces
SER33_YEAST
51,189.50
9
0


cerevisiae GN = SER33 PE = 1 SV = 1






Coatomer subunit beta OS = Saccharomyces cerevisiae GN = SEC26
COPB_YEAST
109,023.60
9
0


PE = 1 SV = 2






Dipeptidyl aminopeptidase B OS = Saccharomyces cerevisiae
DAP2_YEAST
93,406.70
9
0


GN = DAP2 PE = 2 SV = 2






Protein UTH1 OS = Saccharomyces cerevisiae (strain RM11-1a)
UTH1_YEAS1
36,735.90
9
0


GN = UTH1 PE = 3 SV = 1
(+3)





Uncharacterized oxidoreductase YML125C OS = Saccharomyces
YMM5_YEAST
35,388.60
9
0


cerevisiae GN = YML125C PE = 1 SV = 1






Long-chain-fatty-acid-CoA ligase 3 OS = Saccharomyces cerevisiae
LCF3_YEAST
77,948.60
9
0


GN = FAA3 PE = 1 SV = 1






Actin-related protein 2/3 complex subunit 2 OS = Saccharomyces
ARPC2_YEAST
39,567.70
18
1


cerevisiae GN = ARC35 PE = 1 SV = 1






Ceramide very long chain fatty acid hydroxylase SCS7
SCS7_YEAST
44,882.80
9
0


OS = Saccharomyces cerevisiae GN = SCS7 PE = 1 SV = 1






Protein SDS24 OS = Saccharomyces cerevisiae (strain YJM789)
SDS24_YEAS7
57,188.20
9
0


GN = SDS24 PE = 3 SV = 1
(+1)





Cytochrome c oxidase assembly protein COX14 OS = Saccharomyces
COX14_YEAST
7,959.10
9
0


cerevisiae GN = COX14 PE = 1 SV = 1






Signal recognition particle subunit SRP14 OS = Saccharomyces
SRP14_YEAST
16,430.30
9
0


cerevisiae GN = SRP14 PE = 1 SV = 1






Putative guanine nucleotide-exchange factor SED4
SED4_YEAST
114,081.60
9
0


OS = Saccharomyces cerevisiae GN = SED4 PE = 1 SV = 1






Cytochrome b-c1 complex subunit 1, mitochondrial
QCR1_YEAST
50,229.00
71
4


OS = Saccharomyces cerevisiae GN = COR1 PE = 1 SV = 1






Lysyl-tRNA synthetase, cytoplasmic OS = Saccharomyces cerevisiae
SYKC_YEAST
67,960.50
88
5


GN = KRS1 PE = 1 SV = 2






Glutamyl-tRNA synthetase, cytoplasmic OS = Saccharomyces
SYEC_YEAST
80,846.20
246
14


cerevisiae GN = GUS1 PE = 1 SV = 3






Protein transport protein SEC13 OS = Saccharomyces cerevisiae
SEC13_YEAST
33,042.60
35
2


GN = SEC13 PE = 1 SV = 1






Threonyl-tRNA synthetase, cytoplasmic OS = Saccharomyces
SYTC_YEAST
84,522.60
121
7


cerevisiae GN = THS1 PE = 1 SV = 2






Uncharacterized protein YMR178W OS = Saccharomyces cerevisiae
YM44_YEAST
31,145.60
51
3


GN = YMR178W PE = 1 SV = 1






40S ribosomal protein S25-A OS = Saccharomyces cerevisiae
RS25A_YEAST
12,039.90
68
4


GN = RPS25A PE = 1 SV = 1
(+1)





Transposon TY2-LR2 Gag-Pol polyprotein OS = Saccharomyces
YL21B_YEAST
202,130.30
17
1


cerevisiae GN = TY2B-LR1 PE = 3 SV = 1






Farnesyl pyrophosphate synthase OS = Saccharomyces cerevisiae
FPPS_YEAST
40,485.30
135
8


GN = FPP1 PE = 1 SV = 2






Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial
IDH2_YEAST
39,740.60
151
9


OS = Saccharomyces cerevisiae GN = IDH2 PE = 1 SV = 1






Nascent polypeptide-associated complex subunit beta-1
NACB1_YEAS7
17,020.50
33
2


OS = Saccharomyces cerevisiae (strain YJM789) GN = EGD1 PE = 3
(+1)





SV = 1






40S ribosomal protein S3 OS = Saccharomyces cerevisiae GN = RPS3
RS3_YEAST
26,503.00
296
18


PE = 1 SV = 5






ATP-dependent RNA helicase SUB2 OS = Saccharomyces cerevisiae
SUB2_YEAS7
50,280.10
49
3


(strain YJM789) GN = SUB2 PE = 3 SV = 1
(+1)





Elongation factor 1-gamma 2 OS = Saccharomyces cerevisae
EF1G2_YEAST
46,521.90
98
6


GN = TEF4 PE = 1 SV = 1






















Fold





NSAF
NSAF
enriched




Protein
TAL-PrA
Wild type
TAL-PrA/WT
Rank
Rank/N





Plasma membrane ATPase 1 OS = Saccharomyces
0.00300044
2.19206E-05
136.8778684
1
0.001956947


cerevisiae GN = PMA1 PE = 1 SV = 2







Transposon Ty1-H Gag-Pol polyprotein
0.000721016
1.07667E-05
66.96712916
2
0.003913894


OS = Saccharomyces cerevisiae GN = TY1B-H PE = 1







SV = 1







ATP-dependent RNA helicase DED1
0.002132761
3.33122E-05
64.02351908
3
0.005870841


OS = Saccharomyces cerevisiae (strain YJM789)







GN = DED1 PE = 3 SV = 1







Protein TIF31 OS = Saccharomyces cerevisiae
0.000833936
1.50427E-05
55.43798971
4
0.007827789


GN = TIF31 PE = 1 SV = 1







Protein URA1 OS = Saccharomyces cerevisiae
0.002963245
5.34515E-05
55.43798971
5
0.009784736


GN = URA2 PE = 1 SV = 4







Elongation factor 3B OS = Saccharomyces cerevisiae
0.001017068
1.88464E-05
53.96618467
6
0.011741683


GN = HEF3 PE = 1 SV = 2







Transposon Ty1-OL Gag polyprotein
0.002361064
4.4561E-05
52.98498131
7
0.01369863


OS = Saccharomyces cerevisiae GN = TY1A-OL PE = 1







SV = 1







40S ribosomal protein S1-B OS = Saccharomyces
0.003792691
7.57911E-05
50.04137124
8
0.015655577


cerevisiae (strain RM11-1a) GN = RPS1B PE = 3 SV = 1







40S ribosomal protein S1-A OS = Saccharomyces
0.003522263
7.59733E-05
46.36185865
9
0.017612524


cerevisiae (strain RM11-1a) GN = RPS1A PE = 3 SV = 1







Transposon Ty1-DR3 Gag polyprotein
0.002047426
4.43968E-05
46.11655781
10
0.019569472


OS = Saccharomyces cerevisiae GN = TY1A-DR3 PE = 1







SV = 1







Galactose transporter OS = Saccharomyces cerevisiae
0.001540685
3.43213E-05
44.89005361
11
0.021526419


GN = GAL2 PE = 1 SV = 3







Argininosuccinate synthase OS = Saccharomyces
0.002019878
4.65214E-05
43.41824857
12
0.023483366


cerevisiae GN = ARG1 PE = 1 SV = 2







Pleiotropic ABC efflux transporter of multiple drugs
0.000477712
1.28122E-05
37.28572759
13
0.025440313


OS = Saccharomyces cerevisiae GN = PDR5 PE = 1 SV = 1







1,3-beta-glucan synthase compnent FKS1
0.000376467
1.01637E-05
37.04042675
14
0.02739726


OS = Saccharomyces cerevisiae GN = FKS1 PE = 1 SV = 2







Heat shock protein SSC3, mitochondrial
0.001146459
3.11579E-05
36.79512591
15
0.029354207


OS = Saccharomyces cerevisiae GN = ECM10 PE = 1 SV = 1







Pyruvate decarboxylase isozyme 3 OS = Saccharomyces
0.001304785
3.54608E-05
36.79512591
16
0.031311155


cerevisiae GN = PDC6 PE = 1 SV = 3







Nuclear segregation protein BFR1 OS = Saccharomyces
0.001343076
3.99651E-05
33.606215
17
0.033268102


cerevisiae GN = BFR1 PE = SV = 1







60S ribosomal protein L18 OS = Saccharomyces
0.003360413
0.000106195
31.64380828
18
0.035225049


cerevisiae GN = RPL18A PE = 1 SV = 1







40S ribosomal protein S2 OS = Saccharomyces
0.002458834
7.95536E-05
30.90790577
19
0.037181996


cerevisiae GN = RPS2 PE = 1 SV = 3







1,3-beta-glucan synthase component GSC2
0.000311042
1.00635E-05
30.90790577
20
0.039138943


OS = Saccharomyces cerevisiae GN = GSC2 PE = 1 SV = 2







6-phosphogluconate dehydrogenase, decarboxylating 2
0.001172178
4.0496E-05
28.94549905
21
0.04109589


OS = Saccharomyces cerevisiae GN = GND2 PE = 1 SV = 1







High-affinity hexose transporter HXT6
0.00092217
3.48087E-05
26.49249066
22
0.043052838


OS = Saccharomyces cerevisiae GN = HXT7 PE = 1 SV = 1







Protein GAL3 OS = Saccharomyces cerevisiae GN = GAL3
0.000986018
3.75666E-05
26.24718982
23
0.056009785


PE = 1 SV = 2







ATP-dependent RNA halicase MSS116, mitochondrial
0.000737438
2.8631E-05
25.75658814
24
0.046966732


OS = Saccharomyces cerevisiae GN = MSS116 PE = 1







SV = 1







Probable cation-transporting ATPase 1
0.000388073
1.61431E-05
24.03948226
25
0.048923679


OS = Saccharomyces cerevisiae GN = SPF1 PE = 1 SV = 1







High-affinity hexose transporter HXT6
0.000837185
3.48254E-05
24.03948226
26
0.050880626


OS = Saccharomyces cerevisiae GN = HXT6 PE = 1 SV = 2







Eukaryotic translation initiation factor 5B
0.000467585
1.94507E-05
24.03948226
26
0.050880626


OS = Saccharomyces cerevisiae GN = FUN12 PE = 1 SV = 2







DNA-directed RNA polymerase II subunit RPB1
0.000268377
1.13966E-05
23.54888058
28
0.054794521


OS = Saccharomyces cerevisiae GN = RPB1 PE = 1 SV = 2







1,3-beta-glucanosyltransferase GAS1
0.0008451
3.66506E-05
23.0582789
29
0.056761468


OS = Saccharomyces cerevisiae GN = GAS1 PE = 1 SV = 2







Eukaryotic translation initiation factor 3 subunit B
0.00056527
2.47784E-05
22.81297806
30
0.058708415


OS = Saccharomyces cerevisiae (strain YJM789)







GN = PRT1 PE = 3 SV = 1







Phosphoglucomutase-1OS = Saccharomyces cerevisiae
0.000772352
3.45999E-05
22.32237639
31
0.060665362


GN = PGM1 PE = 1 SV = 1







T-complex protein 1 subunit gamma
0.000819711
3.71295E-05
22.07707555
32
0.062622309


OS = Saccharomyces cerevisiae GN = CCT3 PE = 1 SV = 2







FACT complex subunit SPT16 OS = Saccharomyces
0.000397347
1.84072E-05
21.58647387
33
0.64579256


cerevisiae GN = SPT16 PE = 1 SV = 1







ATP-dependent RNA helicase DBP1
0.000685433
3.21179E-05
21.34117303
34
0.066536204


OS = Saccharomyces cerevisiae (strain YJM789)







GN = DBP1 PE = 3 SV = 1







Dihydrolipoyllysine-residue acetyltransferase component
0.00089935
4.21415E-05
21.34117303
34
0.066536204


of pyruvate dehydrogenase complex, mitochondrial







OS = Saccharomyces cerevisiae GN = PDA2 PE = 1 SV = 1







Clathrin heave chain OS = Saccharomyces cerevisiae
0.000494931
2.33254E-05
21.21852261
36
0.070450098


GN = CHC1 PE = 1 SV = 1







40S ribosomal protein S8 OS = Saccharomyces
0.002048356
9.70975E-05
21.98587219
37
0.072407045


cerevisiae GN = RPS8A PE = 1 SV = 3







DNA-directed RNA polymerase II subunit RPB2
0.000328146
1.5738E-05
20.85057135
38
0.074363992


OS = Saccharomyces cerevisiae GN = RPB2 PE = 1 SV = 2







Glutamine synthetase OS = Saccharomyces cerevisiae
0.00102603
5.22842E-05
19.62406715
39
0.076320939


GN = GLN1 PE = 1 SV = 2







Mitochondrial import receptor subunit TOM40
0.001006641
5.19456E-05
19.37876631
40
0.078277886


OS = Saccharomyces cerevisiae GN = TOM40 PE = 1 SV = 1







C-1-tetrahydrofolate synthase, cytoplasmic
0.000398323
2.1366E-05
18.64286379
41
0.080234834


OS = Saccharomyces cerevisiae GN = ADE3 PE = 1 SV = 1







rRNA 2′-O-methyltransferase fibrillarin
0.001165684
6.33608E-05
18.39756296
42
0.082191781


OS = Saccharomyces cerevisiae GN = NOP1 PE = 1 SV = 1







Protein SCP160 OS = Saccharomyces cerevisiae
0.001192042
6.47935E-05
18.39756296
42
0.082191781


GN = SCP160 PE = 1 SV = 3







Protein transport protein 56 OS = Saccharomyces cerevisiae
0.000687645
3.8401E-05
17.90696128
44
0.086105675


cerevisiae GN = SEC23 PE = 1 SV = 1







Nucleolar protein 56 OS = Saccharomyces cerevisiae
0.000687645
3.8401E-05
17.90696128
45
0.088062622


GN = NOP56 PE = 1 SV = 1







Orotidine 5′-phosphate decarboxylase
0.001300706
7.4683E-05
17.4163596
46
0.090019569


OS = Saccharomyces cerevisiae GN = URA3 PE = 1 SV = 2







Homocitrate synthase, cytosolic isozyme
0.000773374
4.63641E-05
16.68045708
47
0.091976517


OS = Saccharomyces cerevisiae GN = LYS20 PE = 1 SV = 1







External NADH-ubiquinone oxidoreductase 1,
0.000571718
3.47863E-05
16.43515624
48
0.093933464


mitochondrial OS = Saccharomyces cerevisiae GN = NDE1







PE = 1 SV = 1







Eukaryotic translation initiation factor 3 subunit C
0.000384987
2.34246E-05
16.43515624
49
0.095890411


OS = Saccharomyces cerevisiae (strain YJM789)







GN = NIP1 PE = 3 SV = 1







Zuotin OS = Saccharomyces cerevisiae GN = ZUO1 PE = 1
0.00072121
4.4547E-05
16.1898554
50
0.097847358


SV = 1







Trehalose-phosphatase OS = Saccharomyces cerevisiae
0.000327715
2.12059E-05
15.45395288
51
0.099804305


GN = TPS2 PE = 1 SV = 3







Saccharopepsin OS = Saccharomyces cerevisiae
0.000758359
4.90722E-05
15.45395288
51
0.99804305


GN = PEP4 PE = 1 SV = 1







rRNA biogenesis protein RRP5 OS = Saccharomyces
0.000174731
1.13065E-05
15.45395288
53
0.1037182


cerevisiae GN = RRP5 PE = 1 SV = 1







cAMP-dependent protein kinase regulatory subunit
0.000703343
4.62462E-05
15.20865204
54
0.105675147


OS = Saccharomyces cerevisiae GN = BCY1 PE = 1 SV = 4







Galactokinase OS = Saccharomyces cerevisiae
0.012480213
0.000829109
15.05255151
55
0.107632094


GN = GAL1 PE = 1 SV = 4







Probable 2-methylcitrate dehydratase
0.000566456
3.78562E-05
14.9633512
56
0.109589041


OS = Saccharmyces cerevisiae GN = PDH1 PE = 1 SV = 1







2-isopropylmalate synthase 2, mitochondrial
0.000486249
3.2496E-05
14.9633512
57
0.11545988


OS = Saccharomyces cerevisiae GN = LEU9 PE = 1 SV = 1







NADH-cytochrome b5 reductase 2 OS = Saccharomyces
0.000957996
6.40228E-05
14.9633512
58
0.113502935


cerevisiae (strain YJM789) GN = MCR1 PE = 2 SV = 1







6,7-dimethyl-8-ribityllumazine synthase
0.00017321121
0.00117687
14.71805036
59
0.115459883


OS = Saccharomyces cerevisiae GN = RIB4 PE = 1 SV = 2







N-(5′-phosphoribosyl)anthranilate isomerase
0.001331159
9.0444E-05
14.71805036
59
0.115459883


OS = Saccharomyces cerevisiae GN = TRP1 PE = 1 SV = 2







Glutamate synthase [NADH] OS = Saccharomyces
0.000130484
9.17129E-06
14.22744869
61
0.119373777


cerevisiae GN = GLT1 PE = 1 SV = 2







Nuclear localization sequence-binding protein
0.000661538
4.90335E-05
13.49154617
62
0.121330724


OS = Saccharomyces cerevisiae GN = NSR1 PE = 1 SV = 1







V-type proton ATPase subunit a, vacuolar isoform
0.000308399
2.28587E-05
13.49154617
62
0.121330724


OS = Saccharomyces cerevisiae GN = VPH1 PE = 1 SV = 3







4-aminobutyrate aminotransferase OS = Saccharomyces
0.000556432
4.1243E-05
13.49154617
64
0.125244618


cerevisiae GN = UGA1 PE = 1 SV = 2







Dihydroorotate dehydrogenase OS = Saccharomyces
0.000831161
6.27469E-05
13.24624533
65
0.127201566


cerevisiae GN = URA1 PE = 1 SV = 1







Eukaryotic translation initiation factor 2A
0.000405663
3.06247E-05
13.24624533
66
0.129158513


OS = Saccharomyces cerevisiae GN = YGR054W PE = 1







SV = 1







60S ribosomal protein L32 OS = Saccharomyces
0.00192197
0.000147833
13.00094449
67
0.13111546


cerevisiae GN = RPL32 PE = 1 SV = 1







60S ribosomal protein L15-A OS = Saccharomyces
0.002303041
0.000178831
12.87829407
68
0.133072407


cerevisiae GN = RPL15A PE = 1 SV = 3







Mitochondrial import receptor subunit TOM70
0.000389459
3.11398E-05
12.51034281
69
0.135029354


OS = Saccharomyces cerevisiae (strain YJM789)







GN = TOM70 PE = 3 SV = 1







Mitochondrial acidic protein MAM33
0.000906643
7.24715E-05
12.51034281
70
0.136986301


OS = Saccharomyces cerevisiae FN = MAM33 PE = 1







SV = 1







H/ACA ribonucleoprotein complex subunit 4
0.000499387
3.99179E-05
12.51034281
70
0.136986301


OS = Saccharomyces cerevisiae GN = CBF5 PE = 1 SV = 1







60S ribosomal protein L8-A OS = Saccharomyces
0.003828248
0.000310574
12.32636718
72
0.140900196


cerevisiae GN = RPL8A PE = 1 SV = 4







Eukaryotic translation initiation factor 2 subunit alpha
0.000771455
6.28987E-05
12.26504197
73
0.142857143


OS = Saccharomyces cerevisiae GN = SUI2 PE = 1 SV = 1







NADPH--cytochrome P450 reductasse
0.000348866
2.84439E-05
12.26504197
74
0.14481409


OS = Saccharomyces cerevisiae GN = NCP1 PE = 1 SV = 3







Nucleolar protein 58 OS = Saccharomyces cerevisiae
0.000921641
7.66773E-05
12.01974113
75
0.146771037


(strain YJM789) GN = NOP58 PE = 3 SV = 1







60S ribosomal protein L14-B OS = Saccharomyces
0.003429032
0.000288224
11.89709071
76
0.148727984


cerevisiae GN = RPL14B PE = 1 SV = 1







Pentafunctional AROM polypeptide OS = Saccharomyces
0.00029733
2.49918E-05
11.89709071
76
0.148727984


cerevisiae GN = ARO1 PE = 1 SV = 1







60S ribosomal protein L8-B OS = Saccharomyces
0.00367754
0.000310714
11.8357655
78
0.152641879


cerevisiae GN = RPL8B PE = 1 SV = 3







GTP-binding protein RHO1 OS = Saccharomyces
0.001110598
9.43228E-05
11.77444029
79
0.154598826


cerevisiae GN = RHO1 PE = 1 SV = 3







Invertase 2 OS = Saccharomyces cerevisiae GN = SUC2
0.000424013
3.60113E-05
11.77444029
80
0.156555773


PE = 1 SV = 1







Squalene synthase OS = Saccharomyces cerevisiae
0.000497125
4.22207E-05
11.77444029
80
0.156555773


GN = ERG9 PE = 1 SV = 2







Eukaryotic translation initiation factor 3 subunit B
0.000577426
4.95569E-05
11.65178987
82
0.160469667


OS = Saccharomyces cerevisiae GN = PRT1 PE = 1 SV = 1







Cytochrome c iso-2 OS = Saccharomyces cerevisiae
0.00200888
0.000174244
11.52913945
83
0.162426614


GN = CYC7 PE = 1 SV = 1







ATP-dependent permease PDR15 OS = Saccharomyces
0.000146155
1.2677E-05
11.52913945
84
0.164383562


cerevisiae GN = PDR15 PE = 1 SV = 1







60S ribosomal protein L28 OS = Saccharomyces
0.001473501
0.000130585
11.28383861
85
0.166340509


cerevisiae GN = RPL28 PE = 1 SV = 2







Methionyl-tRNA synthetase, cytoplasmic
0.000287593
2.54871E-05
11.28383861
86
0.1628297456


OS = Saccharomyces cerevisiae GN = MES1 PE = 1 SV = 4







Eukaryotic translation initiation factor 3 subunit G
0.000790304
7.1595E-05
11.03853777
87
0.170254403


OS = Saccharomyces cerevisiae GN = TIF35 PE = 1 SV = 1







General transcriptional corepressor TUP1
0.000307833
2.78871E-05
11.03853777
88
0.17221135


OS = Saccharomyces cerevisiae GN = TUP1 PE = 1 SV = 2







Heat shock protein 42 OS = Saccharomyces cerevisiae
0.000550472
5.10016E-05
10.79323693
89
0.174168297


GN = HSP42 PE = 1 SV = 1







60S ribosomal protein L15-B OS = Saccharomyces
0.001842433
0.000178831
10.30263526
90
0.176125245


cerevisiae GN = RPL15B PE = 1 SV = 2







40S ribosomal protein S23 OS = Saccharomyces
0.001402798
0.000136159
10.30263526
90
0.176125245


cerevisiae GN = RPS23A PE = 1 SV = 1







T-complex protein 1 subunit theta OS = Saccharomyces
0.000364859
3.54141E-05
10.30263526
92
0.180039139


cerevisiae GN = CCT8 PE = 1 SV = 1







26S protease regulatory subunit 8 homolog
0.000485124
4.82358E-05
10.05733442
93
0.181996086


OS = Saccharomyces cerevisiae GN = RPT6 PE = 1 SV = 4







SDO1-like protein YHR087W OS = Saccharomyces
0.001828741
0.000181832
10.05733442
94
0.183953033


cerevisiae GN = YHR087W PE = 1 SV = 1







Mitochondrial escape protein 2 OS = Saccharomyces
0.000221602
2.25847E-05
9.812033576
95
0.18590998


cerevisiae GN = YME2 PE = 1 SV = 1







Alpha-soluble NSF attachment protein
0.000653179
6.65692E-05
9.812033676
95
0.18590998


OS = Saccharomyces cerevisiae GN = SEC17 PE = 1 SV = 4







Protein translocation protein SEC63
0.000284375
2.89823E-05
9.812033576
95
0.18590998


OS = Saccharomyces cerevisiae GN = SEC63 PE = 1 SV = 2







Delta-1-pyrroline-5-carboxylate dehydrogenase,
0.000332526
3.38896E-05
9.812033576
98
0.191780822


mitochondrial OS = Saccharomyces cerevisiae GN = PUT2







PE = 1 SV = 2







Polyamine N-acetyltransferase 1 OS = Saccharomyces
0.001928069
0.000198988
9.689383157
99
0.193737769


cerevisiae GN = PAA1 PE = 1 SV = 1







40S ribosomal protein S22-B OS = Saccharomyces
0.002893283
0.000298603
9.689383157
99
0.193737789


cerevisiae GN = RPS22B PE = 1 SV = 3







Phosphoinositide phosphatase SAC1
0.000286194
3.07028E-05
9.321431897
101
0.197651663


OS = Saccharomyces cerevisiae GN = SAC1 PE = 1 SV = 1







40S ribosomal protein S26-A OS = Saccharomyces
0.001507278
0.0001617
9.321431897
101
0.197651663


cerevisiae GN = RPS26A PE = 1 SV = 1







26S proteasome regulatory subunit RPN2
0.000390567
4.18999E-05
9.321431897
101
0.197651663


OS = Saccharomyces cerevisiae GN = RPN2 PE = 1 SV = 4







Translational activator GCN1 OS = Saccharomyces
6.86049E-05
7.35991E-06
9.321431897
101
0.197651663


cerevisiae GN = GCN1 PE = 1 SV = 1







Dolichyl-diphosphooligosaccharide--protein
0.000249663
2.67838E-05
9.321431897
105
0.205479452


glycosyltransferase subunit STT3 OS = Saccharomyces







cerevisiae GN = STT3 PE = 1 SV = 2







1,3-beta-glucanosyltransferase GAS5
0.000392433
4.21001E-05
9.321431897
105
0.205479452


OS = Saccharomyces cerevisiae GN = GAS5 PE = 1 SV = 1







Acyl-CoA-binding protein OS = Saccharomyces
0.002023076
0.000217035
9.321431897
107
0.209393346


cerevisiae GN = ACB1 PE = 1 SV = 3







Tricalbin-1 OS = Saccharomyces cerevisiae GN = TCB1
0.000148375
1.63478E-05
9.076131058
108
0.211350294


PE = 1 SV = 1







NADP-specific glutamate dehydrogenase 2
0.000399377
4.4003E-05
9.076131058
108
0.211350294


OS = Saccharomyces cerevisiae GN = GDH3 PE = 1 SV = 1







Dolichyl-phosphate-mannose--protein
0.00021386
2.35629E-05
9.076131058
110
0.215264188


mannosyltransferase 1 OS = Saccharomyces cerevisiae







GN = PMT1 PE = 1 SV = 1







Mitochondrial import inner membrane translocase
0.001923423
0.000211921
9.076131058
110
0.215264188


subunit TIM10 OS = Saccharomyces cerevisiae







GN = MRS11 PE = 1 SV = 1







Ornithine carbamoyltransferase OS = Saccharomyces
0.000523699
5.77006E-05
9.076131058
110
0.215264188


cerevisiae GN = ARG3 PE = 1 SV = 1







Putative magnesium-dependent phosphatase YER134C
0.000943354
0.000106825
8.830830219
113
0.221135029


OS = Saccharomyces cerevisiae GN = YER134C PE = 1







SV = 1







Eukaryotic translation initiation factor 4B
0.000397433
4.50051E-05
8.830830219
113
0.221135029


OS = Saccharomyces cerevisiae GN = TIF3 PE = 1 SV = 1







Mitochondrial escape protein 2 OS = Saccharomyces
0.000199503
2.25917E-05
8.830830219
115
0.225048924


cerevisiae (strain YJM789) GN = YME2 PE = 3 SV = 1







Vesicle-associated membrane protein-associated protein
0.000716233
8.11059E-05
8.830830219
115
0.225048924


SCS2 OS = Saccharomyces cerevisiae GN = SCS2 PE = 1







SV = 3







Importin beta SMX1 OS = Saccharomyces cerevisiae
0.000177883
2.01434E-05
8.830830219
115
0.225048924


GN = SXM1 PE = 1 SV = 1







Inorganic phosphate transport protein PHO88
0.000912311
0.00010331
8.830830219
115
0.225048924


OS = Saccharomyces cerevisiae GN = PHO88 PE = 1 SV = 1







Transcription elongation factor SPT6
0.000225986
2.5951E-05
8.708179799
119
0.232876712


OS = Saccharomyces cerevisiae GN = SPT6 PE = 1 SV = 1







T-complex protein 1 subunit delta OS = Saccharomyces
0.000325467
3.79088E-05
8.585529379
120
0.234833659


cerevisiae GN = CCT4 PE = 1 SV = 2







5′-3′ exoribonuclease 1 OS = Saccharomyces cerevisiae
0.0002137
2.48907E-05
8.585529379
120
0.234833659


GN = KEM1 PE = 1 SV = 1







Fumarate reductase OS = Saccharomyces cerevisiae
0.000368743
4.29494E-05
8.585529379
122
0.238747554


GN = YEL047C PE = 1 SV = 1







3-hydroxy-3-methylglutaryl-coenzyme A reductase 1
0.000157513
1.88859E-05
8.34022854
123
0.240704501


OS = Saccharomyces cerevisiae GN = HMG1 PE = 1 SV = 1







26S proteasome regulatory subunit RPN9
0.000397789
4.76952E-05
8.34022854
123
0.240704501


OS = Saccharomyces cerevisiae GN = RPN9 PE = 1 SV = 1







Dolichyl-phosphate-mannose--protein
0.000209652
2.51375E-05
8.34022854
123
0.240704501


mannosyltransferase 2 OS = Saccharomyces cerevisiae







GN = PMT2 PE = 1 SV = 2







Bifunctional protein GAL10 OS = Saccharomyces
0.006432474
0.000781936
8.226338864
126
0.246575342


cerevisiae GN = GAL10 PE = 1 SV = 2







ATP-dependent bile acid permease OS = Saccharomyces
9.3446E-05
1.15438E-05
8.0949277
127
0.24853229


cerevisiae GN = YBT1 PE = 1 SV = 2







Saccharopine dehydrogenase [NAD+, L-lysine-forming]
0.000426308
5.26636E-05
8.0949277
127
0.24853229


OS = Saccharomyces cerevisiae GN = LYS1 PE = 1 SV = 3







Coatomer subunit gamma OS = Saccharomyces
0.000163509
2.08302E-05
7.849626861
129
0.252446184


cerevisiae GN = SEC21 PE = 1 SV = 2







Cell division control protein 53 OS = Saccharomyces
0.000182456
2.3244E-05
7.849626861
129
0.252446184


cerevisiae GN = CDC53 PE = 1 SV = 1







Rotenone-insensitive NADH-ubiquinone oxidoreductase,
0.000299404
3.81424E-05
7.849626861
131
0.256360078


mitochondrial OS = Saccharomyces cerevisiae GN = NDI1







PE = 1 SV = 1







Argininosuccinate lyase OS = Saccharomyces cerevisiae
0.000329703
4.20024E-05
7.849626861
131
0.256360078


GN = ARG4 PE = 1 SV = 2







Zinc finger protein GIS2 OS = Saccharomyces cerevisiae
0.000970965
0.000127686
7.604326022
133
0.260273973


GN = GIS2 PE = 1 SV = 1







Protein kinase MCK1 OS = Saccharomyces cerevisiae
0.000384952
5.06228E-05
7.604326022
133
0.260273973


GN = MCK1 PE = 1 SV = 1







Malate dehydrogenase, peroxisomal
0.000446552
5.87235E-05
7.604326022
135
0.264187867


OS = Saccharomyces cerevisiae GN = MDH3 PE = 1 SV = 3







T-complex protein 1 subunit zeta OS = Saccharomyces
0.000277109
3.6441E-05
7.604326022
136
0.266144814


cerevisiae GN = CCT6 PE = 1 SV = 1







ATP-dependent RNA helicase DBP2
0.000263443
3.57987E-05
7.359025182
137
0.268101761


OS = Saccharomyces cerevisiae GN = DBP2 PE = 1 SV = 1







Cytochrome B pre-mRNA-processing protein 6
0.000860311
0.000116906
7.359025182
138
0.270058708


OS = Saccharomyces cerevisiae GN = CBP6 PE = 1 SV = 1







Protein DCS2 OS = Saccharomyces cerevisiae
0.000392517
5.33382E-05
7.359025182
138
0.270058708


GN = DCS2 PE = 1 SV = 3







Eukaryotic translation initiation factor 3 subunit A
0.000854379
0.000118738
7.195491289
140
0.273972603


OS = Saccharomyces cerevisiae GN = TIF32 PE = 1 SV = 1







Glucose-signaling factor 2 OS = Saccharomyces
0.000677298
9.521E-05
7.11374343
141
0.27592955


cerevisiae GN = GSF2 PE = 1 SV = 1







Glycerol-3-phosphate dehydrogenase [NAD+] 2,
0.000314327
4.41859E-05
7.113724343
142
0.277886497


mitochondrial OS = Saccharomyces cerevisiae







GN = GPD2 PE = 1 SV = 2







Prohibitin-2 OS = Saccharomyces cerevisiae GN = PHB2
0.000451495
6.34682E-05
7.113724343
142
0.277886497


PE = 1 SV = 2







40S ribosomal protein S29-A OS = Saccharomyces
0.002332289
0.000327858
7.113724343
142
0.277886497


cerevisiae GN = RPS29A PE = 1 SV = 3







DNA-directed RNA polymerase I subunit RPA1
8.33248E-05
1.17132E-05
7.113724343
145
0.283757339


OS = Saccharomyces cerevisiae GN = RPA1 PE = 1 SV = 2







Protein transport protein SEC24 OS = Saccharomyces
0.000149893
2.10709E-05
7.113724343
145
0.283757339


cerevisiae GN = SEC24 PE = 1 SV = 1







Carboxypeptidase Y OS = Saccharomyces cerevisiae
0.000250804
3.65156E-05
6.868423503
147
0.287671233


GN = PRC1 PE = 1 SV = 1







V-type proton ATPase subunit d OS = Saccharomyces
0.000376931
5.48789E-05
6.868423503
148
0.28962818


cerevisiae GN = VMA6 PE = 1 SV = 2







Uncharacterized protein YJL171C OS = Saccharomyces
0.000348696
5.0768E-05
6.868423503
148
0.28962818


cerevisiae GN = YJL171C PE = 1 SV = 1







Vacuolar protein sorting/targeting protein PEP1
8.43666E-04
1.22833E-05
6.868423503
148
0.28962818


OS = Saccharomyces cerevisiae GN = PEP1 PE = 1 SV = 1







FACT complex subunit POB3 OS = Saccharomyces
0.000238097
3.46655E-05
6.868423503
151
0.295499022


cerevisiae GN = POB3 PE = 1 SV = 1







Uncharacterized mitochondrial membrane protein
0.000541502
7.88393E-05
6.868423503
151
0.295499022


FMP10OS = Saccharomyces cerevisiae GN = FMP10







PE = 1 SV = 1







RNA annealing protein YRA1 OS = Saccharomyces
0.000579546
8.75034E-05
6.623122664
153
0.299412916


cerevisiae GN = YRA2 PE = 1 SV = 2







Mitochondrial outer membrane protein OM45
0.000324421
4.8983E-05
6.623122664
154
0.301369863


OS = Saccharomyces cerevisiae GN = OM45 PE = 1 SV = 2







Mitochondrial import receptor subunit TOM5
0.002416716
0.000364891
6.623122664
154
0.301369863


OS = Saccharomyces cerevisiae GN = TOM5 PE = 1 SV = 1







T-complex protein 1 subunit alpha OS = Saccharomyces
0.000239133
3.61058E-05
6.623122664
156
0.305283757


cerevisiae GN = TCP1 PE = 1 SV = 2







Eukaryotic translation initiation factor 1A
0.0007988
0.000125247
6.377821825
157
0.307240705


OS = Saccharomyces cerevisiae GN = TIF11 PE = 1 SV = 1







Protein MSN5 OS = Saccharomyces cerevisiae
9.79948E-05
1.53649E-05
6.377821825
158
0.309197652


GN = MSN5 PE = 1 SV = 1







Putative fatty aldehyde dehydrogenase HFD1
0.000232197
3.6407E-05
6.377821825
158
0.309197652


OS = Saccharomyces cerevisiae GN = HFD1 PE = 1 SV = 1







Ergosterol biosynthetic protein 28 OS = Saccharomyces
0.00081278
0.000127439
6.377821825
158
0.309197652


cerevisiae GN = ERG28 PE = 1 SV = 1







Protein YRO2 OS = Saccharomyces cerevisiae
0.000359689
5.63969E-05
6.377821825
158
0.309197652


GN = YRO2 PE = 1 SV = 1







Methylene-fatty acyl-phospholipid synthase
0.000601597
9.43265E-05
6.377821825
162
0.31702544


OS = Saccharomyces cerevisiae GN = PEM2 PE = 1 SV = 1







Protein MKT1 OS = Saccharomyces cerevisiae
0.000141715
2.31087E-05
6.132520985
163
0.318982387


GN = MKT1 PE = 1 SV = 1







Protein MRH1 OS = Saccharomyces cerevisiae
0.000370021
6.03376E-05
6.132520985
163
0.318982387


GN = MRH1 PE = 1 SV = 1







Eukaryotic translation initiation factor 2 subunit beta
0.000424122
6.91596E-05
6.132520985
165
0.322896282


OS = Saccharomyces cerevisiae GN = SUI3 PE = 1 SV = 2







Peroxiredoxin TSA2 OS = Saccharomyces cerevisiae
0.000594774
0.000101028
5.887220146
166
0.324853229


GN = TSA2 PE = 1 SV = 3







Endoplasmic reticulum veriscle protein 25
0.000533314
9.05884E-05
5.887220146
166
0.324853229


OS = Saccharomyces cerevisiae GN = ERV25 PE = 1 SV = 1







PKHD-type hydroxylase TPA1 OS = Saccharomyces
0.000173629
2.94925E-05
5.887220146
166
0.324853229


cerevisiae GN = TPA1 PE = 1 SV = 1







SED5-binding protein 3 OS = Saccharomyces cerevisiae
0.000123674
2.10071E-05
5.887220146
169
0.33072407


GN = SFB3 PE = 1 SV = 1







D-lactate dehydrogenase [cytochrome] 3
0.000232791
3.95417E-05
5.887220146
169
0.33072407


OS = Saccharomyces cerevisiae GN = DLD3 PE = 1 SV = 1







Single-stranded nucleic acid-binding protein
0.00076317
0.00013239
5.764569726
171
0.334637965


OS = Saccharomyces cerevisiae GN = SBP1 PE = 1 SV = 2







Protein CWH43 OS = Saccharomyces cerevisiae
0.000114198
2.02411E-05
5.641919306
172
0.336594912


GN = CWH43 PE = 1 SV = 2







T-complex protein 1 subunit eta OS = Saccharomyces
0.000206247
3.65562E-05
5.641919306
172
0.336594912


cerevisiae GN = CCT7 PE = 1 SV = 1







26S protease regulatory subunit 6B homolog
0.000256832
4.55221E-05
5.641919306
172
0.336594912


OS = Saccharomyces cerevisiae GN = RPT3 PE = 1 SV = 1







NADH-cytochrome b5 reductase 1 OS = Saccharomyces
0.000391195
6.93372E-05
5.641919306
172
0.336594912


cerevisiae GN = CBR1 PE = 1 SV = 2







Glycogen debranching enzyme OS = Saccharomyces
0.000140824
2.49603E-05
5.641919306
176
0.344422701


cerevisiae GN = GDB1 PE = 1 SV = 1







C-5 sterol desaturase OS = Saccharomyces cerevisiae
0.000288325
5.1104E-05
5.641919306
176
0.344422701


GN = ERG3 PE = 1 SV = 1







13 kDa ribonucleoprotein-associated protein
0.00090797
0.000160933
5.641919306
176
0.344422701


OS = Saccharomyces cerevisiae GN = SNU13 PE = 1 SV = 1







UPF0202 protein KRE33 OS = Saccharomyces
0.000103228
1.82965E-04
5.641919306
176
0.344422701


cerevisiae GN = KRE33 PE = 1 SV = 1







Protein phosphatase PP2A regulatory subunit A
0.00017364
3.07768E-05
5.641919306
176
0.344422701


OS = Saccharomyces cerevisiae GN = TPD3 PE = 1 SV = 2







Eukaryotic translation initiation factor 2 subunit gamma
0.000212912
3.77375E-05
5.641919306
176
0.344422701


OS = Saccharomyces cerevisiae GN = GCD11 PE = 1 SV = 1







Midasin OS = Saccharomyces cerevisiae GN = MDN1
2.20277E-05
3.90429E-06
5.641919306
182
0.356164384


PE = 1 SV = 1







Galactose-1-phosphate uridylyltransferase
0.005800888
0.001030416
5.629654264
183
0.358121331


OS = Saccharomyces cerevisiae GN = GAL7 PE = 1 SV = 4







UPF0121 membrane protein YLL023C
0.000366131
6.778446E-05
5.396618467
184
0.360078278


OS = Saccharomyces cerevisiae GN = YLL023C PE = 1







SV = 1







Phosphatidylinositol transfer protein PDR16
0.000289444
5.36342E-05
5.396618467
184
0.360078278


OS = Saccharomyces cerevisiae GN = PDR16 PE = 1 SV = 1







60S ribosomal protein L43 OS = Saccharomyces
0.001167888
0.000216411
5.396618467
186
0.363992172


cerevisiae GN = RPL43A PE = 1 SV = 2







Arginine biosynthesis bifunctional protein ARG7,
0.000246288
4.456375E-05
5.396618467
186
0.363992172


mitochondrial OS = Saccharomyces cerevisiae







GN = ARG7 PE = 1 SV = 1







Probable family 17 glucosidase SCW4
0.00029336
5.436E-05
5.396618467
186
0.363992172


OS = Saccharomyces cerevisiae GN =SCW4 PE = 1 SV = 1







26S protease subunit RPT4 OS = Saccharomyces
0.000238513
4.41967E-05
5.396618467
189
0.369863014


cerevisiae GN = RPT4 PE = 1 SV = 4







60S ribosomal protein L3 OS = Saccharomyces
0.002680969
0.000499055
5.372088383
190
0.371819961


cerevisiae GN = RPL3 PR = 1 SV = 4







Phosphoglucomutase-2 OS = Saccharomyces cerevisiae
0.002929237
0.000553804
5.28929935
191
0.373776908


GN = PGM2 PE = 1 SV = 1







Uncharacterized phosphatase YNL010W
0.000838173
0.000158927
5.273968047
192
0.375733855


OS = Saccharomyces cerevisiae GN = YNL010W PE = 1







SV = 1







Elongation factor 3A OS = Saccharomyces cerevisiae
0.004119318
0.000790698
5.209722589
193
0.377690802


GN = YEF3 PE = 1 SV = 3







Casein kinase II subunit alpha′ OS = Saccharomyces
0.000285478
5.54184E-05
5.151317628
194
0.37964775


cerevisiae GN = CKA2 PE = 1 SV = 2







54S ribosomal protein L12, mitochondrial
0.000544737
0.000105747
5.151317628
194
0.37964775


OS = Saccharomyces cerevisiae GN = MNP1 PE = 1 SV = 1







Nuclear protein SNF4 OS = Saccharomyces cerevisiae
0.000309024
5.99893E-05
5.151317628
194
0.37964775


GN = SNF4 PE = 1 SV = 1







Eukaryotic initiation factor 4F subunit p150
0.000105031
2.03892E-05
5.151317628
194
0.37964775


OS = Saccharomyces cerevisiae GN = TIF4631 PE = 1







SV = 2







Medium-chain fatty acid ethyl ester synthase/esterase 2
0.000219468
4.26042E-05
5.151317628
194
0.37964775


OS = Saccharomyces cerevisiae GN = EHT1 PE = 1 SV = 1







ABC transporter ATP-binding protein ARB1
0.000164512
3.19359E-05
5.151317628
194
0.37964775


OS = Saccharomyces cerevisiae GN = ARB1 PE = 1 SV = 1







Cysteinyl-tRNA synthetase OS = Saccharomyces
0.000128513
2.49476E-05
5.151317628
194
0.37964775


cereviaie GN = YNL247W PE = 1 SV = 1







Protein TTP1 OS = Saccharomyces cerevisiae GN = TTP1
0.000165973
3.22195E-05
5.151317628
194
0.37964775


PE = 1 SV = 1







26S proteasome regulatory subunit RPN8
0.000293607
5.69966E-05
5.151317628
194
0.37964775


OS = Saccharomyces cerevisiae GN = RPN8 PE = 1 SV = 3







NADH-cytochrome b5 reductase 1 OS = Saccharomyces
0.000357999
6.94965E-05
5.151317628
194
0.37964775


cerevisiae (strain YJM789) GN = CBR1 PE = 2 SV = 2







ER membrane protein complex subunit 1
0.000129027
2.50474E-05
5.151317628
204
0.399217221


OS = Saccharomyces cerevisiae GN = EMC1 PE = 1 SV = 1







Heat shock protein 78, mitochondrial
0.001712467
0.00033471
5.11627465
205
0.401174168


OS = Saccharomyces cerevisiae GN = HSP78 PE = 1 SV = 2







Nuclear protein STH1/NPS1 OS = Saccharomyces
6.83479E-05
1.39314E-05
4.906016788
206
0.403131115


cerevisiae GN = STH1 PE = 1 SV = 1







mRNA-binding protein PUF3 OS = Saccharomyces
0.000109244
2.22674E-05
4.906016788
206
0.403131115


cerevisiae GN = PUF3 PE = 1 SV = 1







Actin-interacting protein 1 OS = Saccharomyces
0.00015913
3.24356E-05
4.906016788
206
0.403131115


cerevisiae GN = AIP1 PE = 1 SV = 1







Cytochrome c iso-1 OS = Saccharomyces cerevisiae
0.003517692
0.000717016
4.906016788
206
0.403131115


GN = CYC1 PE = 1 SV = 2







CTP synthase 1 OS = Saccharomyces cerevisiae
0.000165559
3.37461E-05
4.906016788
206
0.403131115


GN = URA7 PE = 1 SV = 2







Squalene monooxygenase OS = Saccharomyces
0.000194343
3.96131E-05
4.906016788
206
0.403131115


cerevisiae GN = ERG1 PE = 1 SV = 2







Putative aldehyde dehydrogenase-like protein YHR039C
0.000150213
3.06181E-05
4.906016788
212
0.414872798


OS = Saccharomyces cerevisiae GN = MSC7 PE = 1 SV = 1







Glucosamine--fructose-6-phosphate aminotransferase
0.000521969
0.000109122
4.783366368
213
0.416829746


[isomerizing] OS = Saccharomyces cerevisiae GN = GFA1







PE = 1 SV = 4







Uncharacterized GTP-binding protein OLA1
0.001879535
0.000395467
4.752703763
214
0.418786693


OS = Saccharomyces cerevisiae GN = OLA1 PE = 1 SV = 1







Probable 1-acyl-sn-glycerol-3-phosphate acyltransferase
0.000300341
6.44409E-05
4.660715949
215
0.42074364


OS = Saccharomyces cerevisiae GN = SLC1 PE = 1 SV = 1







Sporulation-specific protein 21 OS = Saccharomyces
0.000145644
3.12494E-05
4.660715949
216
0.422700587


cerevisiae GN = SPO21 PE = 1 SV = 1







Cell division control protein 42 OS = Saccharomyces
0.000477329
0.000102415
4.660715949
216
0.422700587


cerevisiae GN = CDC42 PE = 1 SV = 2







Serine/threonine-protein phosphatase PP-Z2
0.000129664
2.78207E-05
4.660715949
216
0.422700587


OS = Saccharomyces cerevisiae GN = PPZ2 PE = 1 SV = 4







Putative mitochondrial carrier protein YHM1/SHM1
0.0003064
6.57409E-05
4.660715949
216
0.422700587


OS = Saccharomyces cerevisiae GN = YHM1 PE = 1 SV = 1







60S ribosomal protein L24-A OS = Saccharomyces
0.001155633
0.000247952
4.660715949
216
0.422700587


cerevisiae GN = RPL24A PE = 1 SV = 1







60S ribosomal protein L35 OS = Saccharomyces
0.001463371
0.00031398
4.660715949
216
0.422700587


cerevisiae GN = RPL35A PE = 1 SV = 1







Mitochondrial respiratory chain complexes assembly
0.000109111
2.34108E-05
4.660715949
222
0.43444227


protein RCA1 OS = Saccharomyces cerevisiae







GN = RCA1 PE = 1 SV = 2







Prohibitin-1 OS = Saccharomyces cerevisiae GN = PHB1
0.000647698
0.00013897
4.660715949
222
0.43444227


PE = 1 SV = 2







T-complex protein 1 subunit epsilon
0.000164381
3.52695E-05
4.660715949
222
0.43444227


OS = Saccharomyces cerevisiae GN = CCT5 PE = 1 SV = 3







Translation machinery-associated protein 22
0.000452437
9.70746E-05
4.660715949
222
0.43444227


OS = Saccharomyces cerevisiae (strain YJM789)







GN = TMA22 PE = 3 SV = 1







DnaJ homolog 1, mitochondrial OS = Saccharomyces
0.000183181
3.93031E-05
4.660715949
222
0.43444227


cerevisiae GN = MDJ1 PE = 1 SV = 1







Alpha, alpha-trehalose-phosphate synthase [UDP-
0.000725072
0.000155571
4.660715949
222
0.43444227


forming] 56 kDa subunit OS = Saccharomyces cerevisiae







GN = TPS1 PE = 1 SV = 2







Acetyl-coenzyme A synthetase 2 OS = Saccharomyces
0.001617845
0.000347124
4.660715949
222
0.43444227


cerevisiae GN = ACS2 PE = 1 SV = 1







60S ribosomal protein L24-B OS = Saccharomyces
0.001159999
0.000248889
4.660715949
222
0.43444227


cerevisiae GN = RPL24B PE = 1 SV = 1







Protein YGP1 OS = Saccharomyces cerevisiae
0.00027266
5.85018E-05
4.660715949
222
0.43444227


GN = YGP1 PE = 1 SV = 2







Actin-related protein 2/3 complex subunit 3
0.000494562
0.000106113
4.660715949
231
0.452054795


OS = Saccharomyces cerevisiae GN = ARC18 PE = 1 SV = 1







Isoleucyl-tRNA synthetase, cytoplasmic
0.001141147
0.000248582
4.590629995
232
0.454011742


OS = Saccharomyces cerevisiae GN = ILS1 PE = 1 SV = 1







Eukaryotic translation initiation factor 3 subunit I
0.000511405
0.000112692
4.538065529
233
0.455968689


OS = Saccharomyces cerevisiae (strain YJM789)







GN = TIF34 PE = 3 SV = 1







Dolichol-phosphate mannosyltransferase
0.001287884
0.000287683
4.476740319
234
0.457925636


OS = Saccharomyces cerevisiae GN = DPM1 PE = 1 SV = 3







40S ribosomal protein S29-B OS = Saccharomyces
0.001433232
0.000324597
4.415415109
235
0.459882583


cerevisiae GN = RPS29B PE = 1 SV = 3







Pre-mRNA-splicing factor ATP-dependent RNA helicase
0.000110115
2.49388E-05
4.415415109
236
0.46183953


PRP43 OS = Saccharomyces cerevisiae GN = PRP43







PE = 1 SV = 1







Translocation protein SEC72 OS = Saccharomyces
0.000446225
0.000101061
4.415415109
236
0.46183953


cerevisiae GN = SEC72 PE = 1 SV = 3







Transcription elongation factor SPT5
0.000166746
3.77645E-05
4.415415109
236
0.46183953


OS = Saccharomyces cerevisiae GN = SPT5 PE = 1 SV = 1







Endoplasmic reticulum transmembrane protein 1
0.000411557
9.32092E-05
4.415415109
236
0.46183953


OS = Saccharomyces cerevisiae GN = YET1 PE = 1 SV = 1







Ferrochelatase, mitochondrial OS = Saccharomyces
0.000216204
4.89658E-05
4.415415109
236
0.46183953


cerevisiae GN = HEM15 PE = 1 SV = 1







Protein CBP3, mitochondrial OS = Saccharomyces
0.000246696
5.58715E-05
4.415415109
236
0.46183953


cerevisiae GN = CBP3 PE = 1 SV = 1







Putative protein disulfide-isomerase YIL005W
0.000118712
2.68857E-05
4.415415109
236
0.46183953


OS = Saccharomyces cerevisiae GN = YIL005W PE = 1







SV = 1







Mitochondrial protein import protein MAS5
0.000863384
0.000195539
4.415415109
236
0.46183953


OS = Saccharomyces cerevisiae GN = YDJ1 PE = 1 SV = 1







Peroxisomal-coenzyme A synthetase
0.000159402
3.61013E-05
4.415415109
236
0.46183953


OS = Saccharomyces cerevisiae GN = FAT2 PE = 1 SV = 1







Nuclear cap-binding protein complex subunit 1
0.000192799
4.36651E-05
4.415415109
245
0.479452055


OS = Saccharomyces cerevisiae GN = STO1 PE = 1 SV = 2







Proteasome component Y13 OS = Saccharomyces
0.000335781
7.60474E-05
4.415415109
245
0.479452055


cerevisiae GN = PRE9 PE = 1 SV = 1







Trehalose synthase complex regulatory subunit TSL1
0.000304804
7.10041E-05
4.29276469
247
0.483365949


OS = Saccharomyces cerevisiae GN = TSL1 PE = 1 SV = 1







Ribosomal RNA-processing protein 12
6.62221E-05
1.58802E-05
4.17011427
248
0.485322896


OS = Saccharomyces cerevisiae GN = RRP12 PE = 1 SV = 1







U3 small nucleolar RNA-associated protein 22
6.48185E-05
1.55436E-05
4.17011427
248
0.485322896


OS = Saccharomyces cerevisiae GN = UTP22 PE = 1 SV = 1







40S ribosomal protein S26-B OS = Saccharomyces
0.001354434
0.000324795
4.17011427
248
0.485322896


cerevisiae GN = RPS268PE = SV = 1







Elongator complex protein 1 OS = Saccharomyces
5.95221E-05
1.42735E-05
4.17011427
248
0.485322896


cerevisiae GN = IKI3 PE = 1 SV = 1







Probable 1,3-beta-glucanosyltransferase GAS3
0.0001603338
3.84492E-05
4.17011427
252
0.493150685


OS = Saccharomyces cerevisiae GN = GAS3 PE = 1 SV = 1







Dynamin-related protein DNM1 OS = Saccharomyces
0.000428661
0.000102794
4.17011427
252
0.493150685


cerevisiae GN = DNM1 PE = 1 SV = 1







Pyruvate dehydrogenase complexs protein X component,
0.000401489
9.62777E-05
4.17011427
252
0.493150685


mitochondrial OS = Saccharomyces cerevisiae GN = PDX1







PE = 1 SV = 1







GTP-binding protein RHO3 OS = Saccharomyces
0.00035976
8.6271E-05
4.17011427
252
0.493150685


cerevisiae GN = RHO3 PE = 1 SV = 2







DNA-directed RNA polymerase I subunit RPA2
0.000130225
3.21744E-05
4.04746385
256
0.500978474


OS = Saccharomyces cerevisiae GN = RPA2 PE = 1 SV = 1







54S ribosomal protein YmL6, mitochondrial
0.000268086
6.83055E-05
3.92481343
257
0.502935421


OS = Saccharomyces cerevisiae GN = YML6 PE = 1 SV = 2







ER-derived vesicles protein ERV29 OS = Saccharomyces
0.000244777
6.23666E-05
3.92481343
257
0.502935421


cerevisiae GN = ERV29 PE = 1 SV = 1







54S ribosomal protein L3, mitochondrial
0.000194787
4.96296E-05
3.92481343
257
0.502935421


OS =Saccharomyces cerevisiae GN = MRPL3 PE = 1 SV = 2







Pyrroline-5-carboxylate reductase OS = Saccharomyces
0.000284449
7.24746E-05
3.92481343
257
0.502935421


cerevisiae GN = PRO3 PE = 1 SV = 1







60S ribosomal protein L34-A OS = Saccharomyces
0.000628399
0.000160109
3.92481343
257
0.502935421


cerevisiae GN = RPL34A PE = 1 SV = 1







Serine/threonine-protein kinase YPK1
0.000112061
2.85519E-05
3.92481343
257
0.502935421


OS =Saccharomyces cerevisiae GN = YPK1 PE = 1 SV = 2







60S ribosomal protein L19 OS = Saccharomyces
0.000789773
0.000201226
3.92481343
257
0.502935421


cerevisiae GN = RPL19A PE = 1 SV = 5







CDP-diacylglycerol--inositol 3-phosphatidyltransferase
0.000345261
8.79687E-05
3.92481343
264
0.516634051


OS = Saccharomyces cerevisiae GN = PIS1 PE = 1 SV = 1







60S ribosome subunit biogeneses protein NIP7
0.00042053
0.000107146
3.92481343
264
0.516634051


OS = Saccharomyces cerevisiae GN = NIP7 PE = 1 SV = 1







Cell division control protein 10 OS = Saccharomyces
0.00023148
5.89787E-05
3.92481343
264
0.516634051


cerevisiae GN = CDC10 PE = 1 SV = 1







E3 ubiquitin-protein ligase RSP5 OS = Saccharomyces
9.33468E-05
2.37837E-05
3.92481343
264
0.516634051


cerevisiae GN = RSP5 PE = 1 SV = 1







Glucan 1,3-beta-glucosidase I/II OS = Saccharomyces
0.000167033
4.25582E-05
3.92481343
264
0.516634051


cerevisiae GN = EXG1 PE = 1 SV = 1







Eukaryotic translation initiation factor 5A-2
0.010829628
0.002807121
3.857913202
269
0.526418787


OS = Saccharomyces cerevisiae GN = HYP2 PE = 1 SV = 3







1,4-alpha-glucan-branching enzyme
0.000204713
5.38413E-05
3.802163011
270
0.52875734


OS = Saccharomyces cerevisiae GN = GLC3 PE = 1 SV = 2







Polyadenylate-binding protein, cytoplasmic and nuclear
0.001523484
0.000407257
3.740837801
271
0.530332681


OS = Saccharomyces cerevisiae GN = PAB1 PE = 1 SV = 4







Protein GCY OS = Saccharomyces cerevisiae GN = GCY1
0.004153505
0.001120519
3.70676824
272
0.532289628


PE = 1 SV = 1







Putative thiosulfate sulfurtransferase YOR285W
0.001042629
0.000283361
3.679512591
273
0.534246575


OS = Saccharomyces cerevisiae GN = YOR285W PE = 1







SV = 1







DNA topoisomerase 2-associated protein PAT1
9.07936E-05
2.46754E-05
3.679512591
274
0.536203523


OS = Saccharomyces cerevisiae GN = PAT1 PE = 1 SV = 3







CAAX prenyl protease 1 OS = Saccharomyces cerevisiae
0.000153556
4.17326E-05
3.679512591
274
0.536203523


GN = STE24 PE = 1 SV = 1







Endoplasmic reticulum transmembrane protein 3
0.000350817
9.53433E-05
3.679512591
274
0.536203523


OS = Saccharomyces cerevisiae GN = YET3 PE = 1 SV = 1







ATP-dependent RNA helicase DOB1
6.58304E-05
1.78911E-05
3.679512591
277
0.542074364


OS = Saccharomyces cerevisiae GN = MTR4 PE = 1 SV = 1







Translation machinery-associated protein 17
0.000479086
0.000130204
3.679512591
277
0.542074364


OS = Saccharomyces cerevisiae GN = TMA17 PE = 1 SV = 1







Carbon catabolite-derepressing protein kinase
0.000111525
3.03099E-05
3.679512591
277
0.542074364


OS = Saccharomyces cerevisiae GN = SNF1 PE = 1 SV = 1







tRNA (cytosinw-5-)-methyltransferase NCL1
0.000103174
2.80402E-05
3.679512591
277
0.542074364


OS = Saccharomyces cerevisiae GN = NCL1 PE = 1 SV = 1







Protein transport protein SEC61 OS = Saccharomyces
0.000151778
4.12496E-05
3.679512591
277
0.542074364


cerevisiae GN = SEC61 PE = 1 SV = 1







Calcineurin subunit B OS = Saccharomyces cerevisiae
0.000409121
0.000111189
3.679512591
277
0.542074364


GN = CNB1 PE = 1 SV = 3







Lysophospholipase 1 OS = Saccharomyces cerevisiae
0.000112114
3.04697E-05
3.679512591
277
0.542074364


GN = PLB1 PE = 1 SV = 2







Proteasome component Y7 OS = Saccharomyces
0.000295812
8.03944E-05
3.679512591
277
0.542074364


cerevisiae GN = PRE8 PE = 1 SV = 1







Metal resistance protein YCF1 OS = Saccharomyces
4.69538E-05
1.27609E-05
3.679512591
277
0.542074364


cerevisiae GN = YCF1 PE = 1 SV = 2







Ran GTPase-activating protein 1 OS = Saccharomyces
0.000175372
4.76619E-05
3.679512591
277
0.542074364


cerevisiae GN = RNA1 PE = 1 SV = 2







L-aminoadipate-semialdehyde dehydrogenase
0.000103446
2.81139E-05
3.679512591
277
0.542074364


OS = Saccharomyces cerevisiae GN = LYS2 PE = 1 SV = 2







Serine hydroxymethyltransferase, mitochondrial
0.000299329
8.13501E-05
3.679512591
288
0.563600783


OS = Saccharomyces cerevisiae GN = SHM1 PE = 1 SV = 2







Coatomer subunit alpha OS = Saccharomyces cerevisiae
0.000351559
9.66186E-05
3.638629118
289
0.56555773


GN = RET1 PE = 1 SV = 2







40S ribosomal protein S10-B OS = Saccharomyces
0.003742563
0.001028564
3.638629118
289
0.56555773


cerevisiae GN = RPS10B PE = 1 SV = 1







40S ribosomal protein S10-A OS = Saccharomyces
0.003742269
0.001028483
3.638629118
289
0.56555773


cerevisiae GN = RPS10A PE = 1 SV = 1







Tryptophan synthase OS = Saccharomyces cerevisiae
0.000412455
0.000113995
3.618187381
292
0.571428571


GN = TRP5 PE = 1 SV = 1







Serine/threonine-protein phosphatase PP1-2
0.000865225
0.000243255
3.556862171
293
0.573385519


OS = Saccharomyces cerevisiae GN = GLC7 PE = 1 SV = 1







Aminopeptidase Y OS = Saccharomyces cerevisiae
0.000258312
7.26236E-05
3.556862171
293
0.573385519


GN = APE3 PE = 1 SV = 1







Glycerol-3-phosphate dehydrogenase [NAD+] 1
0.00143702
0.000407527
3.526199566
295
0.577299413


OS = Saccharomyces cerevisiae GN = GPD1 PE = 1 SV = 4







Valyl-tRNA synthetase, mitochondrial
0.000732554
0.00020835
3.515978698
296
0.57925636


OS = Saccharomyces cerevisiae GN = VAS1 PE = 1 SV = 2







Aconitrate hydratase, mitochondrial OS = Saccharomyces
0.004316972
0.001227815
3.515978698
297
0.581213307


cerevisiae GN = ACO1 PE = 1 SV = 2







Elongation factor Tu, mitochondrial OS = Saccharomyces
0.000636478
0.000182083
3.495536962
298
0.583170254


cerevisiae GN = TUF1 PE = 1 SV = 1







Glycerol-3-phosphate O-acyltransferase 2
8.96548E-05
2.61064E-05
3.434211752
299
0.585127202


OS = Saccharomyces cerevisiae GN = GPT2 PE = 1 SV = 1







Putative ribosomal RNA methyltransferase Nop2
0.000107421
3.12796E-05
3.434211752
299
0.585127202


OS = Saccharomyces cerevisiae GN = NOP2 PE = 1 SV = 1







Serine/threonine-protein kinase YPK2/YKR2
9.78166E-05
2.8483E-05
3.434211752
299
0.585127202


OS = Saccharomyces cerevisiae GN = YPK2 PE = 1 SV = 1







Xanthine phosphoribosyltransferase 1
0.000316809
9.22508E-05
3.434211752
302
0.590998043


OS = Saccharomyces cerevisiae GN = XPT1 PE = 1 SV = 1







3-hydroxy-3-methylgutaryl-coenzyme A reductase 2
6.48202E-05
1.88748E-05
3.434211752
302
0.590998043


OS = Saccharomyces cerevisiae GN = HMG2 PE = 1 SV = 1







3-keto-steroid reductase OS = Saccharomyces cerevisiae
0.000188778
5.49698E-05
3.434211752
302
0.590998043


GN = ERG27 PE = 1 SV = 1







Ras-like protein 2 OS = Saccharomyces cerevisiae
0.000216093
6.29235E-05
3.434211752
302
0.590998043


GN = RAS2 PE = 1 SV = 4







Protein phosphatase 1 regulatory subunit SDS22
0.000192838
5.6152E-05
3.434211752
302
0.590998043


OS = Saccharomyces cerevisiae GN = SDS22 PE = 1 SV = 1







Ubiquitin-like protein SMT3 OS = Saccharomyces
0.001293296
0.00376592
3.434211752
302
0.590998043


cerevisiae GN = SMT3 PE = 1 SV = 1







Sphingosine-1-phosphate lyase OS = Saccharomyces
0.000114378
3.33055E-05
3.434211752
302
0.590998043


cerevisiae GN = DPL1 PE = 1 SV = 1







Protein transport protein SSS1 OS = Saccharomyces
0.000838514
0.000244165
3.434211752
302
0.590998043


cerevisiae GN = SSS1 PE = 1 SV = 2







UPF0674 endoplasmic reticulum membrane protein
0.000159242
4.63692E-05
3.434211752
302
0.590998043


YNR021W OS = Saccharomyces cerevisiae







GN = YNR021W PE = 1 SV = 3







Non-classical export protein 2 OS = Saccharomyces
0.000395383
0.000115131
3.434211752
302
0.590998043


cerevisiae GN = NCE102 PE = 1 SV = 1







Reduced viability upon starvation protein 161
0.000247902
7.21859E-05
3.434211752
302
0.590998043


OS = Saccharomyces cerevisiae GN = RVS161 PE = 1







SV = 1







Cytochrome b5 OS = Saccharomyces cerevisiae
0.000563995
0.000164228
3.434211752
302
0.590998043


GN = CYB5 PE = 1 SV = 2







60S ribosomal protein L37-A OS = Saccharomyces
0.00076134
0.000221693
3.434211752
302
0.590998043


cerevisiae GN = RPL37A PE = 1 SV = 2







Calmodulin OS = Saccharoyces cerevisiae GN = CMD1
0.000464783
0.000135339
3.434211752
302
0.590998043


PE = 1 SV = 1







Actin-related protein 2/3 complex subunit 5
0.000437682
0.000127447
3.434211752
302
0.590998043


OS = Saccharomyces cerevisiae GN = ARC15 PE = 1 SV = 1







Mitochondrial outer membrane protein SCY_3392
9.17107E-05
2.6705E-05
3.434211752
317
0.62035225


OS = Saccharomyces cerevisiae (strain YJM789)







GN = SCY_3392 PE = 3 SV = 1







tRNA pseudouridine synthase 1 OS = Saccharomyces
0.000120677
3.51396E-05
3.434211752
317
0.62035225


cerevisiae GN = PUS1 PE = 1 SV = 1







Heterotrimeric G protein gamma subunit GPG1
0.00050257
0.000146342
3.434211752
317
0.62035225


OS = Saccharomyces cerevisiae GN = GPG1 PE = SV = 1







Anthranilate synthase component 1 OS = Saccharomyces
0.000132104
3.84672E-05
3.434211752
320
0.626223092


cerevisiae GN = TRP2 PE = 1 SV = 4







UPF0662 protein YPL260W OS = Saccharomyces
0.000230371
6.95657E-05
3.311561332
321
0.628180039


cerevisiae GN = YPL260W PE = 1 SV = 1







NADPH-dependent 1-acyldihydroxyacetone phosphate
0.000440749
0.000133094
3.311561332
321
0.6218180039


reductase OS = Saccharomyces cerevisiae GN = AYR1







PE = 1 SV = 1







Long-chain-fatty-acid--CoA ligase 1 OS = Saccharomyces
0.000557224
0.000168266
3.311561332
323
0.632093933


cerevisiae GN = FAA1 PE = 1 SV = 1







Small COPII coat GTPase SAR1 OS = Saccharomyces
0.001323495
0.0004072
3.250236122
324
0.634050881


cerevisiae GN = SAR1 PE = 1 SV = 1







GMP synthase [glutamine-hydrolyzing]
0.000485453
0.000149359
3.250236122
325
0.636007828


OS = Saccharomyces cerevisiae GN = GUA1 PE = 1 SV = 4







Mitochondrial outer membrane protein porin 1
0.003256725
0.001004705
3.241475378
326
0.637964775


OS = Saccharomyces cerevisiae GN = POR1 PE = 1 SV = 4







ATP-dependent helicase NAM7 OS = Saccharomyces
6.36357E-05
1.99553E-05
3.188910912
327
0.639921722


cerevisiae GN = NAM7 PE = 1 SV = 1







Proteasome component PRE2 OS = Saccharomyces
0.000220117
6.90258E-05
3.188910912
327
0.639921722


cerevisiae GN = PRE2 PE = 1 SV = 3







Homocitrate synthase, mitochondrial
0.000859811
0.000269625
3.188910912
327
0.639921722


OS = Saccharomyces cerevisiae GN = LYS21 PE = 1 SV = 1







Nucleolar complex protein 2 OS = Saccharomyces
8.53356E-05
2.67601E-05
3.188910912
330
0.645792564


cerevisiae GN = NOC2 PE = 1 SV = 2







Transcriptional regulatory protein SIN3
3.9829E-05
1.24898E-05
3.188910912
330
0.645792564


OS = Saccharomyces cerevisiae GN = SIN3 PE = 1 SV = 2







Ribosome biogenesis protein ERB1
7.59361E-05
2.38126E-05
3.188910912
330
0.645792564


OS = Saccharomyces cerevisiae (strain YJM789)







GN = ERB1 PE = 3 SV = 1







Dihydroxy-acid dehydratase, mitochondrial
0.000664668
0.000208431
3.188910912
330
0.645792564


OS = Saccharomyces cerevisiae GN = ILV3 PE = 1 SV = 2







Uncharacterized protein YKL054C OS = Saccharomyces
8.29339E-05
2.6007E-05
3.188910912
330
0.645792564


cerevisiae GN = YKL054C PE = 1 SV = 1







DNA-directed RNA polymerases I, II, and III subunit
0.000841244
0.000263803
3.188910912
330
0.645792564


RPABC5 OS = Saccharomyces cerevisiae GN = RPB10







PE = 1 SV = 2







Mitochondrial presequence protease
0.000124148
3.89313E-05
3.188910912
330
0.645792564


OS = Saccharomyces cerevisiae GN = CYM1 PE = 1 SV = 2







Amidophosphoribosyltranferase OS = Saccharomyces
0.000122775
3.85005E-05
3.188910912
330
0.645792564


cerevisiae GN = ADE4 PE = 1 SV = 1







Protein ERP1 OS = Saccharomyces cerevisiae
0.000281662
8.83256E-05
3.188910912
330
0.645792564


GN = ERP1 PE = 1 SV = 1







Hsp90 co-chaperone HCH1 OS = Saccharomyces
0.000403775
0.000126618
3.188910912
330
0.645792564


cerevisiae GN = HCH1 PE = SV = 1







Acetyl-CoA carboxylase OS = Saccharomyces cerevisiae
0.001223872
0.00038379
3.188910912
330
0.645792564


GN = FAS3 PE = 1 SV = 2







Mitochondrial outer membrane protein IML2
8.435558E-05
2.64528E-05
3.188910912
330
0.645792564


OS = Saccharomyces cerevisiae (strain YJM789)







GN = IML2 PE = 3 SV = 1







Choline-phosphate cytidylyltransferase
0.000140944
4.41982E-05
3.188910912
342
0.66927593


OS = Saccharomyces cerevisiae GN = PCT1 PE = 1 SV = 2







Nucleosome assembly protein OS = Saccharomyces
0.000145425
4.56032E-05
3.188910912
342
0.68927593


cerevisiae GN = NAP1 PE = 1 SV = 2







THO complex subunit 2 OS = Saccharomyces cerevisiae
3.78591E-05
1.18721E-05
3.188910912
342
0.66927593


GN = THO2 PE = 1 SV = 1







Sec sixty-one protein homolog OS = Saccharomyces
0.000130618
4.096E-05
3.188910912
342
0.66927593


cerevisiae GN = SSH1 PE = 1 SV = 1







Cytochrome c heme lyase OS = Saccharomyces
0.000231505
7.25968E-05
3.188910912
342
0.66927593


cerevisiae GN = CYC3 PE = 1 SV = 1







Prefoldin subunit 4 OS = Saccharomyces cerevisiae
0.000458719
0.000143848
3.188910912
342
0.66927593


GN = GIM3 PE = 1 SV = 1







Gamma-glutamyl phosphate reductase
0.000139998
4.39016E-05
3.188910912
342
0.66927593


OS = Saccharomyces cerevisiae GN = PRO2 PE = 1 SV = 1







60S ribosomal protein L37-B OS = Saccharomyces
0.000705676
0.000221291
3.188910912
342
0.66927593


cerevisiae GN = RPL37B PE = 1 SV = 2







UPF0368 protein YPL225W OS = Saccharomyces
0.000798365
0.000250357
3.118910912
342
0.66927593


cerevisiae GN = YPL225W PE = 1 SV = 1







Dolichyl-phosphate-mannose--protein
7.91626E-05
2.48243E-05
3.188910912
351
0.686888454


mannosyltransferase 4 OS = Saccharomyces cerevisiae







GN = PMT4 PE = 1 SV = 1







Increased sodium tolerance protein 2
6.57534E-05
2.06194E-05
3.188910912
351
0.686888454


OS = Saccharomyces cerevisiae GN = IST2 PE = 1 SV = 1







Glucokinase-1 OS = Saccharomyces cerevisiae
0.002234448
0.000709793
3.148027439
353
0.690802348


GN = GLK1 PE = 1 SV = 1







Suppressor protein STM1 OS = Saccharomyces
0.003607455
0.001164851
3.096923097
354
0.692759295


cerevisiae GN = STM1 PE = 1 SV = 3







Uridylate kinase OS = Saccharomyces cerevisiae
0.00028029
9.52198E-05
2.943610073
355
0.694716243


GN = URA6 PE = 1 SV = 1







Myosin light chain 1 OS = Saccharomyces cerevisiae
0.00078176
0.000265579
2.943610073
355
0.694716243


GN = MLC1 PE = 1 SV = 1







Glucose-repressible alcohol dehydrogenase
6.78771E-05
2.30591E-05
2.943610073
357
0.698630137


transcriptional effector OS = Saccharomyces cerevisiae







GN = CCR4 PE = 1 SV = 1







54S ribosomal protein L1, mitochondrial
0.000207377
7.04501E-05
2.943610073
357
0.698630137


OS = Saccharomyces cerevisiae GN = MRPL1 PE = 1 SV = 1







Nuclear polyadenylated RNA-binding protein 3
7.10775E-05
2.41464E-05
2.943610073
357
0.698630137


OS = Saccharomyces cerevisiae GN = NAB3 PE = 1 SV = 1







Phosphoglycerate mutase 2 OS = Saccharomyces
0.000178191
6.05348E-05
2.943610073
357
0.698630137


cerevisiae GN = GPM2 PE = 1 SV = 1







3′(2′),5′-bisphosphate nucleotidase OS = Saccharomyces
0.000164191
5.57789E-05
2.943610073
357
0.698630137


cerevisiae GN = HAL2 PE = 1 SV = 1







Protein SEY1 OS = Saccharomyces cerevisiae (strain
7.18829E-05
2.442E-05
2.943610073
357
0.698630137


AWRI1631) GN = SEY1 PE = 3 SV = 1







Thiamine metabolism regulatory protein THI3
9.40228E-05
3.19413E-05
2.943610073
357
0.698630137


OS = Saccharomyces cerevisiae GN = THI3 PE = 1 SV = 1







Alpha-mannosidase OS = Saccharomyces cerevisiae
0.000103261
3.57096E-05
2.943610073
357
0.698630137


GN = AMS1 PE = 1 SV = 2







[NU+] prion formation protein 1 OS = Saccharomyces
4.78514E-05
1.6256E-05
2.943610073
357
0.698630137


cerevisiae GN = NEW1 PE = 1 SV = 1







T-complex protein 1 subunit beta OS = Saccharomyces
0.000112369
3.81738E-05
2.943610073
357
0.698630137


cerevisiae GN = CCT2 PE = 1 SV = 1







Putative zinc metalloproteinase YIL108W
8.30332E-05
2.8208E-05
2.943610073
357
0.698630137


OS = Saccharomyces cerevisiae GN = YIL108W PE = 1







SV = 1







Prefoldin suunit 5 OS = Saccharomyces cerevisiae
0.000350187
0.000118965
2.943610073
357
0.698630137


GN = GIM5 PE = 1 SV = 1







Probable glycosidase CRH2 OS = Saccharomyces
0.000128804
4.37573E-05
2.943610073
357
0.698630137


cerevisiae GN = UTR2 PE = 1 SV = 3







Coatomer subunit epsilon OS = Saccharomyces
0.00019001
6.45499E-05
2.943610073
357
0.698630137


cerevisiae GN = SEC28 PE = 1 SV = 3







26S proteasome regulatory subunit RPN13
0.000359064
0.000121981
2.943610073
357
0.698630137


OS = Saccharomyces cerevisiae GN = RPN13 PE = 1 SV = 1







40S ribosomal protein S28-A OS = Saccharomyces
0.001693466
0.000575302
2.943610073
357
0.698630137


cerevisiae GN = RPS28A PE = 1 SV = 1







D-3-phosphoglycerate dehydrogenase 1
0.000125564
4.26565E-05
2.943610073
357
0.698630137


OS = Saccharomyces cerevisiae GN = SER3 PE = 1 SV = 1







Adenylosuccinate synthetase OS = Saccharomyces
0.000133142
4.52308E-05
2.943610073
357
0.698630137


cerevisiae GN = ADE12 PE = 1 SV = 3







CTP synthase 2 OS = Saccharomyces cerevisiae (strain
9.96651E-05
3.38581E-05
2.943610073
375
0.733855186


YJM789) GN = URA8 PE = 3 SV = 1







ATP-dependent RNA helicase HAS1
0.000113331
3.85006E-05
2.943610073
375
0.733855186


OS = Saccharomyces cerevisiae GN = HAS1 PE = 1 SV = 1







Zinc finger protein ZPR1 OS = Saccharomyces cerevisiae
0.000116721
3.96523E-05
2.943610073
375
0.733855186


GN = ZPR1 PE = 1 SV = 1







26S proteasome regulatory subunit RPN3
0.00010638
3.61393E-05
2.943610073
375
0.733855186


OS = Saccharomyces cerevisiae GN = RPN3 PE = 1 SV = 4







Peroxisomal membrane protein PMP27
0.000239176
8.12526E-05
2.943610073
375
0.733855186


OS = Saccharomyces cerevisiae GN = PEX11 PE = 1 SV = 2







Ribose-phosphate pyrophosphokinase 5
0.000120138
4.08132E-05
2.943610073
375
0.733855186


OS = Saccharomyces cerevisiae GN = PRS5 PE = 1 SV = 1







U6 snRNA-associated Sm-like protein LSm6
0.00068399
0.000232364
2.943610073
375
0.733855186


OS = Saccharomyces cerevisiae (strain YJM789)







GN = LSM6 PE = 3 SV = 1







Protein HMF1 OS = Saccharomyces cerevisiae
0.00046226
0.000157038
2.943610073
375
0.733855186


GN = HMF1 PE = 1 SV = 1







General negative regulator of transcription subunit 1
2.67455E-05
9.08595E-06
2.943610073
375
0.733855186


OS = Saccharomyces cerevisiae GN = NOT1 PE = 1 SV = 2







Putative glucokinase-2 OS = Saccharomyces cerevisiae
0.000881255
0.000312395
2.820959653
384
0.75146771


GN = EMI2 PE = 1 SV = 1







26S protease regulatory subunit 4 homolog
0.000252314
8.94425E-05
2.820959653
385
0.753424658


OS = Saccharomyces cerevisiae GN = RPT2 PE = SV = 3







Sphingolipid long chain base-responsive protein LSP1
0.001589943
0.000573593
2.771899485
386
0.755381605


OS = Saccharomyces cerevisiae GN = LSP1 PE = 1 SV = 1







UPF0001 protein YBL036C OS = Saccharomyces
0.000202322
7.4981E-05
2.698309233
387
0.757338552


cerevisiae GN = YBL036C PE = 1 SV = 1







Galactose/lactose metabolism regulatory protein GAL80
0.000121933
4.51887E-05
2.698309233
388
0.759295499


OS = Saccharomyces cerevisiae GN = GAL80 PE = 1 SV = 2







U3 small nucleolar ribonucleoprotein protein IMP3
0.000269233
9.97785E-05
2.698309233
388
0.759295499


OS = Saccharomyces cerevisiae GN = IMP3 PE = 1 SV = 1







U3 small nucleolar RNA-associated protein 21
5.62287E-05
2.08385E-05
2.698309233
388
0.759295499


OS = Saccharomyces cerevisiae GN = UTP21 PE = 1 SV = 1







DNA polymerase alpha catalytic subunit A
3.53233E-05
1.30909E-05
2.698309233
388
0.759295499


OS = Saccharomyces cerevisiae GN = POL1 PE = 1 SV = 2







Probable glycerophosphodiester phosphodiesterase
0.000158949
5.89071E-05
2.698309233
388
0.759295499


YPL206C OS = Saccharomyces cerevisiae GN = YPL206C







PE = 1 SV = 1







Cytochrome c oxidase assemply protein COX15
0.000107801
3.99514E-05
2.698309233
388
0.759295499


OS = Saccharomyces cerevisiae GN = COX15 PE = 1 SV = 1







U6 snRNA-associated Sm-like protein LSm5
0.000565322
0.00020951
2.698309233
388
0.759295499


OS = Saccharomyces cerevisiae GN = LSM5 PE = 1 SV = 1







60S ribosomal protein L29 OS = Saccharomyces
0.000883547
0.000327445
2.698309233
388
0.759295499


cerevisiae GN = RPL29 PE = 1 SV = 3







Tricalbin-3 OS = Saccharomyces cerevisiae GN = TCB3
6.88849E-05
2.55289E-05
2.698309233
388
0.759295499


PE = 1 SV = 1







Peroxiredoxin HYR1 OS = Saccharomyces cerevisiae
0.000632164
0.000234282
2.698309233
388
0.759295499


GN = HYR1 PE = 1 SV = 1







Glucose-6-phosphate 1-dehydrogenase
0.000409742
0.000151852
2.698309233
388
0.759295499


OS = Saccharomyces cerevisiae GN = ZWF1 PE = 1 SV = 4







Endosomal protein P24B OS = Saccharomyces
0.000252541
9.35923E-05
2.698309233
388
0.759295499


cerevisiae GN = EMP24 PE = 1 SV = 1







Proteasome component C1 OS = Saccharomyces
0.000186846
6.92457E-05
2.698309233
388
0.759295499


cerevisiae GN = PRE10 PE = 1 SV = 2







26S proteasome regulatory subunit RPN6
0.000118379
4.38716E-05
2.698309233
388
0.759295499


OS = Saccharomyces cerevisiae GN = RPN6 PE = 1 SV = 3







Monothiol glutaredoxin-3 OS = Saccharomyces cerevisiae
0.000181409
6.72305E-05
2.698309233
388
0.759295499


GN = GRX3 PE = 1 SV = 1







C-8 sterol isomerase OS = Saccharomyces cerevisiae
0.000236677
8.77132E-05
2.698309233
388
0.759295499


GN = ERG2 PE = 1 SV = 1







Uncharacterized membrane glycoprotein YNR065C
4.70626E-05
1.74415E-05
2.698309233
388
0.759295499


OS = Saccharomyces cerevisiae GN = YNR065C PE = 1







SV = 1







Ubiquitin carboxyl-terminal hydrolase 6
0.000103173
3.82361E-05
2.698309233
405
0.792563601


OS = Saccharomyces cerevisiae GN = UBP6 PE = 1 SV = 1







Histone chaperone ASF1 OS = Saccharomyces
0.000186452
6.90996E-05
2.698309233
405
0.72563601


cerevisiae GN = ASF1 PE = 1 SV = 1







Pumilio homology domain family member 6
0.000156904
5.81491E-05
2.698309233
405
0.792563601


OS = Saccharomyces cerevisiae GN = PUF6 PE = 1 SV = 1







Mitochondrial outer membrane protein OM14
0.00040332
0.000149471
2.698309233
405
0.792563601


OS = Saccharomyces cerevisiae (strain YJM789)







GN = OM14 PE = 3 SV = 1







AP-1 complex subunit gamma-1 OS = Saccharomyces
6.29325E-05
2.332295E-05
2.698309233
405
0.792563601


cerevisiae GN = APL4 PE = 1 SV = 1







Signal recognition particle subunit SRP72
8.01207E-05
2.96929E-05
2.698309233
405
0.792563601


OS = Saccharomyces cerevisiae GN = SRP72 PE = 1 SV = 2







Protein transport protein SEC31 OS = Saccharomyces
4.24814E-05
1.57437E-05
2.698309233
405
0.792563601


cerevisiae GN = SEC31 PE = 1 SV = 2







Phosphatidylethanolamine N-methyltransferase
5.8221E-05
2.15769E-05
2.698309233
405
0.792563601


OS = Saccharomyces cerevisiae GN = PEM1 PE = 1 SV = 1







Mitochondrial import inner membrane translocase
0.000363362
0.000134663
2.698309233
405
0.792563601


subunit TIM16 OS = Saccharomyces cerevisiae







GN = PAM16 PE = 1 SV = 1







Phosphatidate cytidylyltransferase OS = Saccharomyces
0.000113698
4.21366E-05
2.698309233
405
0.792563601


cerevisiae GN = CDS1 PE = 1 SV = 1







26S proteasome regulatory subunit RPN12
0.000184589
6.84093E-05
2.698309233
405
0.792563601


OS = Saccharomyces cerevisiae GN = RPN12 PE = 1 SV = 3







N-terminal acetyltransferase A complex subunit NAT1
5.95728E-05
2.20778E-05
2.698309233
405
0.792563601


OS = Saccharomyces cerevisiae GN = NAT1 PE = 1 SV = 2







Nucleolar pre-ribosomal-associated protein 1
2.89842E-05
1.07416E-05
2.698309233
405
0.792563601


OS = Saccharomyces cerevisiae GN = URB1 PE = 1 SV = 2







GU4 nucleic-binding protein 1 OS = Saccharomyces
0.001107392
0.000415119
2.667646629
418
0.818003914


cerevisiae GN = ARC1 PE = 1 SV = 2







Mitochondrial peculiar membrane protein 1
0.000809029
0.000306801
2.636984024
419
0.819960861


OS = Saccharomyces cerevisiae GN = MPM1 PE = 1 SV = 1







6-phosphogluconate dehydrogenase, decarboxylating 1
0.00494208
0.001876038
2.63431771
420
0.821917808


OS = Saccharomyces cerevisiae GN = GND1 PE = 1 SV = 1







Transcription-associated protein 1 OS = Saccharomyces
2.59681E-05
1.00821E-05
2.575658814
421
0.823874755


cerevisiae GN = TRA1 PE = 1 SV = 1







RNA polymerase-associated protein CTR9
0.000180474
7.00692E-05
2.575658814
421
0.823874755


OS = Saccharomyces cerevisiae GN = CTR9 PE = 1 SV = 2







DNA-directed RNA polymerases I, II, and III subunit
0.000681273
0.000264504
2.575658814
423
0.82778865


RPABC3 OS = Saccharomyces cerevisiae GN = RPB8







PE = 1 SV = 1







Ribonucleoside-diphosphate reductase large chain 1
0.000112985
4.38663E-05
2.575658814
423
0.82778865


OS = Saccharomyces cerevisiae GN = RNR1 PE = 1 SV = 2







60S ribosomal protein L10 OS = Saccharomyces
0.003548365
0.001377653
2.575658814
423
0.82778866


cerevisiae GN = RPL10 PE = 1 SV = 1







Sphingolipid long chain base-responsive protein PIL1
0.002318695
0.00091108
2.544996209
426
0.833659491


OS = Saccharomyces cerevisiae GN = PIL1 PE = 1 SV = 1







Ribosome-associated complex subunit SSZ1
0.001333689
0.000524947
2.540615837
427
0.835616438


OS = Saccharomyces cerevisiae GN = SSZ1 PE = 1 SV = 2







Golgin IMH1 OS = Saccharomyces cerevisiae GN = IMH1
5.09048E-05
2.0752E-05
2.453008394
428
0.837573386


PE = 1 SV = 1







Protein SCO2, mitochondrial OS = Saccharomyces
0.000153531
6.25888E-05
2.453008394
428
0.837573386


cerevisiae GN = SCO2 PE = 1 SV = 1







3-ketoacyl-CoA reductase OS = Saccharomyces
0.000138384
5.64138E-05
2.453008394
428
0.837573386


cerevisiae GN = IFA38 PE = 1 SV = 1







Iron transport multicopper oxidase FET5
7.55744E-05
3.08089E-05
2.453008394
428
0.837573386


OS = Saccharomyces cerevisiae GN = FET5 PE = 1 SV = 1







Protein ISD11 OS = Saccharomyces cerevisiae
0.000475466
0.00019383
2.453008394
428
0.837573386


GN = ISD11 PE = 1 SV = 1







Mitochondrial distribution and morphology protein 38
8.24018E-05
3.35921E-05
2.453008394
428
0.837573386


OS = Saccharomyces cerevisiae GN = MDM38 PE = 1







SV = 1







Elongation of fatty acids protein 3 OS = Saccharomyces
0.000135728
5.53313E-05
2.453008394
428
0.837573386


cerevisiae GN = ELO3 PE = 1 SV = 1







Nucleolar GTP-binding protein 1 OS = Saccharomyces
7.19874E-05
2.93466E-05
2.453008394
428
0.837573386


cerevisiae GN = NOG1 PE = 1 SV = 1







Peptidyl-prolyl cis-trans isomerase ESS1
0.000276053
0.000112537
2.453008394
428
0.837573386


OS = Saccharomyces cerevisiae GN = ESS1 PE = 1 SV = 3







ATPase GET3 OS = Saccharomyces cerevisiae (strain
0.000136114
5.54886E-05
2.453008394
428
0.837573386


RM11-1a) GN = GET3 PE = 3 SV = 1







Protein APA1 OS = Saccharomyces cerevisiae GN = APA1
0.000146785
5.98386E-05
2.453008394
428
0.837573386


PE = 1 SV = 4







Mitochondrial respiratory chain complexes assembly
6.33584E-05
2.58288E-05
2.453008394
439
0.859099804


protein AFG3 OS = Saccharomyces cerevisiae GN = AFG3







PE = 1 SV = 1







Calcium-transporting ATPase 2 OS = Saccharomyces
4.09332E-05
1.6687E-05
2.453008394
439
0.859099804


cereviiae GN = PMC1 PE = 1 SV = 1







Probable intramembrane protease YKL100C
7.93266E-05
3.23385E-05
2.453008394
439
0.859099804


OS = Saccharomyces cerevisiae GN = YKL100C PE = 1







SV = 1







KH domain-containing protein YBL032W
0.000128508
5.23877E-05
2.453008394
439
0.859099804


OS = Saccharomyces cerevisiae GN = YBL032W PE = 1







SV = 1







Mitochondrial import receptor subunit TOM22
0.000319029
0.000130056
2.453008394
439
0.859099804


OS = Saccharomyces cerevisiae GN = TOM22 PE = 1 SV = 3







Protein MSP1 OS = Saccharomyces cerevisiae
0.00013277
5.41252E-05
2.453008394
439
0.859099804


GN = MSP1 PE = 1 SV = 2







UPF0364 protein YMR027W OS = Saccharomyces
9.89598E-05
4.03422E-05
2.453008394
439
0.859099804


cerevisiae GN = YMR027W PE = 1 SV = 1







Uncharacterized protein YJL217W OS = Saccharomyces
0.000243858
9.94119E-0
2.453008394
439
0.859099804


cerevisiae GN = YJL217W PE = 1 SV = 1







ER membrane protein complex subunit 4
0.000249609
0.000101756
2.453008394
439
0.859099804


OS = Saccharomyces cerevisiae GN = EMC4 PE = 1 SV = 1







Sm-like protein LSm1 OS = Saccharomyces cerevisiae
0.000263782
0.000107534
2.453008394
439
0.859099804


GN = LSM1 PE = 1 SV = 1







Probable alphs-1,6-mannosyltransferase MNN10
0.000114582
4.6711E-05
2.453008394
439
0.859099804


OS = Saccharomyces cerevisiae GN = MNN10 PE = 1 SV = 1







Protein HAM1 OS = Saccharomyces cerevisiae
0.000242455
9.884E-05
2.453008394
439
0.859099804


GN = HAM1 PE = 1 SV = 1







NADPH-dependent methylglyoxal reductase GRE2
0.000140339
5.7211E-05
2.453008394
439
0.859099804


OS = Saccharomyces cerevisiae GN = GRE2 PE = 1 SV = 1







Alpha-1,2 mannosyltransferase KTR1
0.000116392
4.74486E-05
2.453008394
439
0.859099804


OS = Saccharomyces cerevisiae GN = KTR1 PE = 1 SV = 1







Protein VTH1 OS = Saccharomyces cerevisiae GN = VTH1
3.07094E-05
1.25191E-05
2.453008394
453
0.886497065


PE = 1 SV = 1







Trehalose synthase complex regulatory subunit TPS3
4.50766E-05
1.8376E-05
2.453008394
453
0.886497065


OS = Saccharomyces cerevisiae GN = TPS3 PE = 1 SV = 3







Heat shock protein 60, mitochondrial
0.006551267
0.002731813
2.398138469
455
0.890410959


OS = Saccharomyces cerevisiae GN = HSP60 PE = 1 SV = 1







Pyruvate dehydrogenase E1 component subunit alphs,
0.001029786
0.000436161
2.361020579
456
0.892367906


mitochondrial OS = Saccharomyces cerevisiae GN = PDB1







PE = 1 SV = 2







Pyruvate dehydrogenase E1 component subunit alpha,
0.00110963
0.000471203
2.354888058
457
0.894324853


mitochondrial OS = Saccharomyces cerevisiae GN = PDA1







PE = 1 SV = 2







Actin-related protein 3 OS = Saccharomyces cerevisiae
0.000205437
8.81567E-05
2.330357974
458
0.8962818


GN = ARP3 PE = 1 SV = 1







AMP deaminase OS = Saccharomyces cerevisiae
0.000109083
4.68094E-05
2.330357974
458
0.8962818


GN = AMD1 PE = 1 SV = 2







Lon protease homolog, mitochondrial
0.000235988
0.000103075
2.289474501
460
0.900195695


OS = Saccharomyces cerevisiae GN = PIM1 PE = 1 SV = 2







Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial
0.003037645
0.001332737
2.279253633
461
0.902152642


OS = Saccharomyces cerevisiae GN = IDH1 PE = 1 SV = 2







Serine hydroxymethyltransferase, cytosolic
0.001128399
0.00501825
2.248591028
462
0.904109589


OS = Saccharomyces cerevisiae GN = SHM2 PE = 1 SV = 2







Rab proteins geranylgeranyltransferase component A
7.15564E-05
3.24121E-05
2.207707555
463
0.906066536


OS = Saccharomyces cerevisiae GN = MRS6 PE = 1 SV = 2







37S ribosomal protein MRP1, mitochondrial
0.000131255
5.9453E-05
2.207707555
463
0.906066536


OS = Saccharomyces cerevisiae GN = MRP1 PE = 1 SV = 2







Carboxypeptidase S OS = Saccharomyces cerevisiae
7.46309E-05
3.38047E-05
2.207707555
463
0.906066536


GN = CPS1 PE = 1 SV = 2







Probable glucose transporter HXT5 OS = Saccharomyces
7.27682E-05
3.2961E-05
2.207707555
466
0.911937378


cerevisiae GN = HXT5 PE = 1 SV = 1







Glycerol-3-phosphate dehydrogenase, mitochondrial
0.000665985
0.000301664
2.207707555
466
0.9119378378


OS = Saccharomyces cerevisiae GN = GUT2 PE = 1 SV = 2







Cytochrome b2, mitochondrial OS = Saccharomyces
7.35584E-05
3.33189E-05
2.207707555
466
0.911937378


cerevisiae GN = CYB2 PE = 1 SV = 1







Translation machinery-associated protein 20
0.000237747
0.00010769
2.207707555
466
0.911937378


OS = Saccharomyces cerevisiae GN = TMA20 PE = 1 SV = 1







D-arabinono-1,4-lactone oxidase OS = Saccharomyces
8.10341E-05
3.67051E-05
2.207707555
466
0.911937378


cerevisiae GN = ALO1 PE = 1 SV = 1







Protein phosphatase 2C homolog 3 OS = Saccharomyces
9.38112E-05
4.24926E-05
2.207707555
466
0.911937378


cerevisiae GN = PTC3 PE = 1 SV = 3







DNA-directed RNA polymerase II subunit RPB9
0.000337423
0.000152839
2.207707555
466
0.911937378


OS = Saccharomyces cerevisiae GN = RPB9 PE = 1 SV = 1







Casein kinase II subunit alpha OS = Saccharomyces
0.000107928
4.88868E-05
2.207707555
466
0.911937378


cerevisiae GN = CKA1 PE = 1 SV = 1







26S protease regulatory subunit 6A OS = Saccharomyces
9.99044E-05
4.52526E-05
2.207707555
466
0.911937378


cerevisiae GN = RPT5 PE = 1 SV = 3







Enoyl reductase TSC13 OS = Saccharomyces cerevisiae
0.000131115
5.93898E-05
2.207707555
466
0.911937378


GN = TSC13 PE = 1 SV = 1







H/ACA ribonucleoprotein complex subunit 2
0.000281572
0.000127541
2.207707555
466
0.911937378


OS = Saccharomyces cerevisiae GN = NHP2 PE = 1 SV = 2







Retrograde regulation protein 2 OS = Saccharomyces
7.35221E-05
3.33024E-05
2.207707555
466
0.911937378


cerevisiae GN = RTG2 PE = 1 SV = 2







Uncharacterized protein YDR476C OS = Saccharomyces
0.000190809
8.64284E-05
2.207707555
466
0.911937378


cerevisiae GN = YDR476C PE = 1 SV = 1







DNA-directed RNA polymerases I and III subunit RPAC2
0.000298504
0.00013521
2.207707555
466
0.911937378


OS = Saccharomyces cerevisiae GN = RPC19 PE = 1 SV = 1







GPI transamidase omponent GPI16
7.00996E-05
3.17522E-05
2.207707555
466
0.911937378


OS = Saccharomyces cerevisiae GN = GPI16 PE = 1 SV = 2







V-type proton ATPase subunit e OS = Saccharomyces
0.000575236
0.000260558
2.207707555
466
0.911937378


cerevisiae GN = VMA9 PE = 1 SV = 1







Cell division control protein 28 OS = Saccharomyces
0.000283067
0.000128217
2.207707555
466
0.911937378


cerevisiae GN = CDC28 PE = 1 SV = 1







Serine/threonine-protein phosphatase 2B catalytic
7.03504E-05
3.18658E-05
2.207707555
466
0.911937378


subunit A2 OS = Saccharomyces cerevisiae GN = CNA2







PE = 1 SV = 2







GTP-binding protein YPT31/YPT8 OS = Saccharomyces
0.000197022
8.92428E-05
2.207707555
466
0.911937378


cerevisiae GN = YPT31 PE = 1 SV = 3







FK506-binding nuclear protein OS = Saccharomyces
0.000103559
4.69079E-05
2.207707555
466
0.911937378


cerevisiae GN = FPR3 PE = 1 SV = 2







D-3-phosphoglycerate dehydrogenase 2
9.41815E-05
4.26603E-05
2.207707555
466
0.911937378


OS = Saccharomyces cerevisiae GN = SER33 PE = 1 SV = 1







Coatomer subunit beta OS = Saccharomyces cerevisiae
4.42208E-05
2.00302E-05
2.207707555
466
0.911937378


BN = SEC26 PE = 1 SV = 2







Dipeptidyl aminopeptidase B OS = Saccharomyces
5.16141E-05
2.33791E-05
2.207707555
466
0.911937378


cerevisiae GN = DAP2 PE = 2 SV = 2







Protein UTH1 OS = Saccharomyces cerevisiae (strain
0.000131237
5.94449E-05
2.207707555
466
0.911937378


RM11-1a) GN = UTH1 PE = 3 SV = 1







Uncharacterized oxidoreductase YML125C
0.000136619
6.18829E-05
2.207707555
490
0.95890411


OS = Saccharomyces cerevisiae GN = YML125C PE = 1







SV = 1







Long-chain-fatty-acid--CoA ligase 3 OS = Saccharomyces
6.18498E-05
2.80154E-05
2.207707555
490
0.95890411


cerevisiae GN = FAA3 PE = 1 SV = 1







Actin-related protein 2/3 complex subunit 2
0.000243689
0.000110381
2.207707555
490
0.95890411


OS = Saccharomyces cerevisiae GN = ARC35 PE = 1 SV = 1







Ceramide very long chain fatty acid hydroxylase SCS7
0.000107415
4.86547E-05
2.207707555
490
0.95890411


OS = Saccharomyces cerevisiae GN = SCS7 PE = 1 SV = 1







Protein SDS24 OS = Saccharomyces cerevisiae (strain
8.43025E-05
3.81855E-05
2.207707555
490
0.95890411


YJM789) GN = SDS24 PE = 3 SV = 1







Cytochrome c oxidase assembly protein COX14
0.000605735
0.000274373
2.207707555
490
0.95890411


OS = Saccharomyces cerevisiae GN = COX14 PE = 1 SV = 1







Signal recognition particle subunit SRP14
0.000293428
0.000132911
2.207707555
490
0.95890411


OS = Saccharomyces cerevisiae GN = SRP14 PE = 1 SV = 1







Putative guanine nucleotide-exchange factor SED4
4.22602E-05
1.91421E-05
2.207707555
497
0.97260274


OS = Saccharomyces cerevisiae GN = SED4 PE = 1 SV = 1







Cytochrome b-c1 complex subunit 1, mitochondrial
0.000757196
0.000347809
2.17704495
498
0.974559687


OS = Saccharomyces cerevisiae GN = COR1 PE = 1 SV = 1







Lysyl-tRNA synthetase, cytoplasmic
0.000693634
0.000321328
2.158647387
499
0.976516634


OS = Saccharomyces cerevisiae GN = KRS1 PE = 1 SV = 2







Glutamyl-tRNA synthetase, cytoplasmic
0.00162997
0.000756317
2.155143089
500
0.978473581


OS = Saccharomyces cerevisiae GN = GUS1 PE = 1 SV = 3







Protein transport protein SEC13 OS = Saccharomyces
0.000567411
0.000264357
2.146382345
501
0.980430528


cerevisiae GN = SEC13 PE = 1 SV = 1







Threonyl-tRNA synthetase, cytoplasmic
0.000766861
0.00036171
2.120100112
502
0.982387476


OS = Saccharomyces cerevisiae GN = THS1 PE = 1 SV = 2







Uncharacterized protein YMR178W OS = Saccharomyces
0.000877158
0.000420688
2.085057135
503
0.984344423


cerevisiae GN = YMR178W PE = 1 SV = 1







40S ribosomal protein S25-A OS = Saccharomyces
0.003025452
0.001451016
2.085057135
503
0.984344423


cerevisiae GN = RPS25A PE = 1 SV = 1







Transposon Ty2-LR1 Gag-Pol polyprotein
4.50528E-05
2.16075E-05
2.085057135
503
0.984344423


OS = Saccharomyces cerevisiae GN = TY2B-LR1 PE = 3







SV = 1







Farnesyl pyrophosphate synthase OS = Saccharomyces
0.001786243
0.000863034
2.069725832
506
0.990215264


cerevisiae GN = FPP1 PE = 1 SV = 2







Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial
0.002035386
0.000989107
2.057801486
507
0.992172211


OS = Saccharomyces cerevisiae GN = IDH2 PE = 1 SV = 1







Nascent polypeptide-associated complex subunit beta-1
0.001038594
0.000513207
2.023731925
508
0.994129159


OS = Saccharomyces cerevisiae (strain YJM789)







GN = EGD1 PE = 3 SV = 1







40S ribosomal protein S3 OS = Saccharomyces
0.00598275
0.002966283
2.016918013
509
0.996086106


cerevisiae GN = RPS3 PE = 1 SV = 5







ATP-dependent RNA helicase SUB2
0.00052204
0.000260592
2.003290188
510
0.998043053


OS = Saccharomyces cerevisiae (strain YJM789)







GN = SUB2 PE = 3 SV = 1







Elongation factor 1-gamma 2 OS = Saccharomyces
0.001128425
0.000563286
2.003290188
510
0.998043053


cerevisiae GN = TEF4 PE = 1 SV = 1





















TABLE 8





Histone PTMs identified from GAL1 promoter chromatin isolated from cells


grown in galactose-containing media.


















Protein
Sequence
Modifications
PTM





Histone H3
(R)EIAQDFkTDLR(F)
Trimethyl (+42)
K79me3



(R)EIAQDFkTDLR(F)
Dimethyl (+28)
K79me2



(R)EIAQDFkTDLR(F)
Methyl (+14)
K79me



(R)FQkSTELLIR(K)
Acetyl (+42)
K56ac



(R)KQLASkAAR(K)
Acetyl (+42)
K23ac



(R)kQLASkAAR(K)
Acetyl (+42), Acetyl (+42)
K18ac K23ac



(R)KSTGGkAPR(K)
Acetyl (+42)
K14ac



(R)kSTGGkAPR(K)
Acetyl (+42), Acetyl (+42)
K9ac K14ac


Histone H2B
(K)AEkKPASkAPAEK(K)
Acetyl (+42), Acetyl (+42)
K6ac K11ac



(K)KPASkAPAEKkPAAK(K)
Acetyl (+42), Acetyl (+42)
K11ac K17ac



(K)APAEKkPAAK(K)
Acetyl (+42)
K17ac


Histone H2A
(K)GGkAGSAAK(A)
Acetyl (+42)
K7ac


Histone H4

None













Histone H3





Sequence
Modifications
PTM
Spectrum ID





(R)EIAQDFkTDLR(F)
Trimethyl (+42)
K79me3
Tackett_051413_L1_21.3892.3892.3.dta


(R)EIAQDFkTDLR(F)
Trimethyl (+42)

Tackett_051413_L1_19.3763.3763.2.dta


(R)EIAQDFkTDLR(F)
Dimethyl (+28)
K79me2
Tackett_051413_L1_21.3948.3948.3.dta


(R)EIAQDFkTDLR(F)
Dimethyl (+28)

Tackett_051413_L1_19.3877.3877.3.dta


(R)EIAQDFkTDLR(F)
Methyl (+14)
K79me
Tackett_051413_L1_19.3827.3827.3.dta


(R)EIAQDFkTDLR(F)
Acetyl (+42)
K79ac
Tackett_051413_L1_19.3776.3776.3.dta


(R)EIAQDFkTDLR(F)
Methyl (+14)

Tackett_051413_L1_19.3815.3815.2.dta


(R)EIAQDFkTDLR(F)
Methyl (+14)

Tackett_051413_L1_19.3832.3832.2.dta


(R)FQkSTELLIR(K)
Acetyl (+42)
K56ac
Tackett_051413_L1_20.5345.5345.2.dta


(R)FQkSTELLIR(K)
Acetyl (+42)

Tackett_051413_L1_19.5128.5128.2.dta


(R)FQkSTELLIR(K)
Acetyl (+42)

Tackett_051413_L1_19.5114.5114.2.dta


(R)KQLASkAAR(K)
Acetyl (+42)
K23ac
Tackett_051413_L1_16.1239.1239.2.dta


(R)KQLASkAAR(K)
Acetyl (+42)

Tackett_051413_L1_01.1032.1032.2.dta


(R)KQLASkAAR(K)
Acetyl (+42)

Tackett_051413_L1_20.1311.1311.2.dta


(R)KQLASkAAR(K)
Acetyl (+42)

Tackett_051413_L1_20.1316.1316.2.dta


(R)kQLASkAAR(K)
Acetyl (+42),
K18ac
Tackett_051413_L1_19.2100.2100.2.dta



Acetyl (+42)
K23ac


(R)KQLASkAAR(K)
Acetyl (+42)

Tackett_051413_L1_19.1327.1327.2.dta


(R)KQLASkAAR(K)
Acetyl (+42)

Tackett_051413_L1_19.1340.1340.2.dta


(R)kQLASkAAR(K)
Acetyl (+42),

Tackett_051413_L1_20.2166.2166.2.dta



Acetyl (+42)


(R)kQLASkAAR(K)
Acetyl (+42),

Tackett_051413_L1_20.2178.2178.2.dta



Acetyl (+42)


(R)KSTGGkAPR(K)
Acetyl (+42)
K14ac
Tackett_051413_L1_20.549.549.2.dta


(R)KSTGGkAPR(K)
Acetyl (+42)

Tackett_051413_L1_23.698.698.2.dta


(R)KSTGGkAPR(K)
Acetyl (+42)

Tackett_051413_L1_22.552.552.2.dta


(R)kSTGGkAPR(K)
Acetyl (+42),
K9ac
Tackett_051413_L1_12.1197.1197.2.dta



Acetyl (+42)
K14ac


(R)KSTGGkAPR(K)
Acetyl (+42)

Tackett_051413_L1_19.506.506.2.dta


(R)kSTGGkAPR(K)
Acetyl (+42),

Tackett_051413_L1_13.1112.1112.2.dta



Acetyl (+42)


(R)KSTGGkAPR(K)
Acetyl (+42)

Tackett_051413_L1_20.438.438.2.dta


(R)KSTGGkAPR(K)
Acetyl (+42)

Tackett_051413_L1_22.555.555.2.dta


(R)KSTGGkAPR(K)
Acetyl (+42)

Tackett_051413_L1_19.623.623.2.dta


(R)KSTGGkAPR(K)
Acetyl (+42)

Tackett_051413_L1_19.627.627.2.dta


(K)STGGkAPR(K)
Acetyl (+42)

Tackett_051413_L1_20.734.734.2.dta


(K)STGGkAPR(K)
Acetyl (+42)

Tackett_051413_L1_19.715.715.2.dta


(K)STGGkAPR(K)
Acetyl (+42)

Tackett_051413_L1_19.720.720.2.dta


(K)STGGkAPR(K)
Acetyl (+42)

Tackett_051413_L1_20.744.744.2.dta


(K)STELLIR(K)


Tackett_051413_L1_16.3348.3348.2.dta


(K)STELLIR(K)


Tackett_051413_L1_19.3325.3325.2.dta


(K)STELLIR(K)


Tackett_051413_L1_20.3349.3349.2.dta

## Claims

1. A method of identifying proteins, including proteins comprising posttranslational modifications, specifically associated with a target chromatin in a cell, the method comprising:
(a) providing:
i) a first cell sample comprising nucleic acid binding proteins and the target chromatin, wherein the target chromatin is tagged by contacting the target chromatin with a tag capable of specifically recognizing and binding one or more portions of the target chromatin and wherein the tag comprises an affinity handle, and
ii) a second cell sample comprising nucleic acid binding proteins and the target chromatin, where in the target chromatin is not tagged,
wherein the first cell sample and the second cell sample are lysed;

(b) performing affinity purification on each lysed cell sample in (a) using a substrate capable of binding the affinity handle, wherein affinity purification of the first cell sample results in isolation of affinity handle bound to tagged target chromatin bound to nucleic acid binding proteins and affinity purification of the second cell sample results in isolation of nucleic acid binding proteins non-specifically bound to the substrate, wherein isolating the affinity handle isolates proteins associated with the tagged target chromatin,
(c) identifying bound proteins from (b),
(d) determining the amount of each bound protein in each sample from (b), wherein bound proteins that are enriched in the first cell sample as compared to the second cell sample are specifically associated with the tagged chromatin in the first cell sample.

2. The method of claim 1, wherein the first cell sample is lysed before tagging the target chromatin.

3. The method of claim 1, wherein the first cell sample is lysed after tagging the target chromatin.

4. The method of claim 3, wherein a target chromatin is tagged by expressing in a cell protein A tagged TAL protein engineered to have binding specificity for a nucleic acid sequence component of the target chromatin.

5. The method of claim 1, wherein the proteins in the first cell sample and the second cell sample are crosslinked before lysis.

6. The method of claim 1, wherein the chromatin in the lysed cell sample from step (a) is fragmented before isolating the tagged target nucleic acid sequence.

7. The method of claim 6, wherein the chromatin in the lysed cell sample is fragmented to comprise nucleic acid sections comprising 500 to 1500 base pairs.

8. The method of claim 1, wherein proteins or protein fragments associated with the target chromatin are identified using mass spectrometry.

9. The method of claim 8, wherein the proteins or protein fragments identified using mass spectrometry are quantified and identified as enriched in the sample containing the tagged target chromatin compared to the sample containing the untagged target chromatin using label-free proteomics.

10. The method of claim 9, wherein the label-free proteomics technique is spectral counting.

11. The method of claim 9, wherein proteins enriched in the sample containing the tagged target chromatin compared to the sample containing the untagged target chromatin are enriched by at least 2 fold.