cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c57k5f
title: MassIVE MSV000083147 - GNPS - ONR Primary Wright - Food
title: Data was collected on a LC-MS/MS system (c18 column) positive mode [dataset license: CC0 1.0 Universal (CC0 1.0)]
DOI: 10.25345/c5cc8r
title: MassIVE MSV000083146 - GNPS - ONR Primary Wright - Human - Stool - QTOF
title: Data was collected on a LC-MS/MS system (c18 column) positive mode [dataset license: CC0 1.0 Universal (CC0 1.0)]
DOI: 10.25345/c5h306
title: MassIVE MSV000083145 - Integrated proteomic/lipidomics reveal that the swarming motility of Paenibacillus polymyxa is driven by phospholipid changes, surfactants, and flagellar specialization
title: To better understand the molecular-level details of the swarming phenotype in P. polymyxa,m this study was designed to use a bioinformatics approach to integrate proteomics and lipidomics datasets generated for P. polymyxa grown in liquid swimming culture bacteria vs. swarming on agar platesbacteria. Integration of omics datasets unraveled the growth condition dependent phospholipid metabolism and possible membrane remodulation. Further, this study identifies the possible roles of GHs, flagellar assembly, chemotaxis and production of wetting agents and surfactants in swarming motility along with the validation from gene expression using RT-PCR.
DOI: 10.25345/c5ms4j
title: MassIVE MSV000083144 - KILchip v1.0 A novel Plasmodium falciparum merozoite protein microarray to facilitate malaria vaccine candidate prioritization
title: KILchip v1.0: a novel protein microarray to facilitate high throughput multiplexed antibody detection from individual samples
DOI: 10.25345/c5rk53
title: MassIVE MSV000083142 - RNAlater test 1 removal
title: Samples from Burkina Faso were treated with RNAlater and underwent an optimized RNAlater removal protocol only once. Previous samples had undergone the removal twice.
DOI: 10.25345/c5w89r
title: MassIVE MSV000083143 - TomahaqCompanion
title: Triggered by Offset, Multiplexed, Accurate mass, High resolution, and Absolute Quantitation (TOMAHAQ) is a recently introduced targeted proteomics method that combines peptide and sample multiplexing. TOMAHAQ assays enable sensitive and accurate multiplexed quantification by implementing an intricate data collection scheme that comprises multiple MSn scans, mass inclusion lists, and data-driven filters.  Consequently, manual creation of TOMAHAQ methods can be time consuming and error prone while the resulting TOMAHAQ data may not be compatible with common mass spectrometry analysis pipelines.  To address these concerns we introduce TomahaqCompanion, an open-source desktop application that enables rapid creation of TOMAHAQ methods and analysis of TOMAHAQ data.  Starting from a list of peptide sequences, a user can perform each step of TOMAHAQ assay development including 1) generation of priming run target list, 2) analysis of priming run data, 3) generation of TOMAHAQ method file, and 4) analysis and export of quantitative TOMAHAQ data.  We demonstrate the flexibility of TomahaqCompanion by creating a variety of methods testing TOMAHAQ parameters (e.g., number of SPS notches, run length, etc.).  Lastly, we analyze an interference sample comprising heavy yeast peptides, a standard human peptide mixture, TMT11-plex, and super heavy TMT (shTMT) isobaric labels to demonstrate ~10-200 attomol limit of quantification within a complex background using TOMAHAQ.
DOI: 10.25989/0gmr-w134
title: Materials Experiment and Analysis Database:
DOI: 10.25989/2c8x-an37
title: Materials Experiment and Analysis Database:
DOI: 10.25989/4mn5-gz09
title: Materials Experiment and Analysis Database:
DOI: 10.25989/6j3y-nn17
title: Materials Experiment and Analysis Database:
DOI: 10.25989/a5yw-az76
title: Materials Experiment and Analysis Database:
DOI: 10.25989/afa9-ge11
title: Materials Experiment and Analysis Database:
DOI: 10.25989/cf6f-1d84
title: Materials Experiment and Analysis Database:
DOI: 10.25989/cz9c-zg77
title: Materials Experiment and Analysis Database:
DOI: 10.25989/h5qd-yq80
title: Materials Experiment and Analysis Database:
DOI: 10.25989/q6c7-5s57
title: Materials Experiment and Analysis Database:
DOI: 10.25989/q6dc-k166
title: Materials Experiment and Analysis Database:
DOI: 10.25989/vdy4-2h76
title: Materials Experiment and Analysis Database:
DOI: 10.25989/wd4h-r428
title: Materials Experiment and Analysis Database:
DOI: 10.25345/c56k6h
title: MassIVE MSV000083153 - MudPIT analyses of the proteins co-purified with Ada2b-PB-FLAG-HA FLAG-affinity purified from Drosophila melanogaster S2 cells
title: Protein Complexes Purification- Stable S2 cell lines expressing Ada2b (isoform B; NP_001027151.1) in the pRmHa3-CHA2FL2 (Ada2b-PBH2F2) were maintained at 1-2 e6 cells/mL in SFX medium (HyQ SFX-Insect). Cells stably transfected with empty vector served as negative controls. Protein complexes containing Ada2b-PB were purified from nuclear extracts (from 12 L of 1e7/L S2 Ada2b-PBH2F2 cells) via their FLAG epitope tag. Isolated complexes were further separated by size on a Superose 6 10/300 gel filtration column. Eluates from the FLAG-IP (input) and size exclusion chromatography (SEC) fractions were TCA-precipitated from proteomics analysis. Two biological replicates of SEC fractions 12 and 19 were analyzed.
Multidimensional Protein Identification Technology- TCA-precipitated protein pellets were solubilized using Tris-HCl pH 8.5 and 8 M urea, followed by addition of TCEP (Tris(2-carboxyethyl)phosphine hydrochloride; Pierce) and CAM (chloroacetamide; Sigma) were added to a final concentration of 5 mM and 10 mM, respectively. Proteins were digested using Endoproteinase Lys-C at 1:100 w/w (Roche) at 37oC overnight. The samples were brought to a final concentration of 2 M urea and 2 mM CaCl2 and a second digestion was performed overnight at 37oC using trypsin (Roche) at 1:100 w/w. The reactions were stopped using formic acid (5% final). The digested size exclusion eluates were loaded on a split-triple-phase fused-silica micro-capillary column and placed in-line with a linear ion trap mass spectrometer (LTQ, Thermo Scientific), coupled with a Quaternary Agilent 1100 Series HPLC system. A fully automated 10-step chromatography run was carried out. Each full MS scan (400-1600 m/z) was followed by five data-dependent MS/MS scans. The number of the micro scans was set to 1 both for MS and MS/MS. The settings were as follows: repeat count 2; repeat duration 30 s; exclusion list size 500 and exclusion duration 120 s, while the minimum signal threshold was set to 100. 
MS Data Processing- The MS/MS data set was searched using ProLuCID (v. 1.3.3) against a database consisting of 21,402 non-redundant Drosophila melanogaster proteins (downloaded from NCI RefSeq 2013-02-20), 177 usual contaminants, and, to estimate false discovery rates (FDRs), 21,579 randomized amino acid sequences derived from each NR protein entry. To account for alkylation by CAM, 57 Da were added statically to the cysteine residues. To account for the oxidation of methionine to methionine sulfoxide, 16 Da were added as a differential modification to the methionine residue. Peptide/spectrum matches were sorted and selected to an FDR less than 5% at the peptide and protein levels, using DTASelect in combination with swallow, an in-house software.
DOI: 10.25345/c5bc8f
title: MassIVE MSV000083152 - GNPS cyanobacteria dereplicatio test 20.11.2018
title: The data will be used to test the dereplication procedure.
DOI: 10.25345/c5g30w
title: MassIVE MSV000083151 - GNPS cyanobacteria 20.11
title: The samples will be used to test the dereplication procedure
DOI: 10.25345/c5kw3w
title: MassIVE MSV000083149 - DART Main Submission
title: Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. Identifying proteins by LC-MS/MS proteomics, however, remains challenging for lowly abundant samples, such as the proteomes of single mammalian cells. To increase the identification rate of peptides in such small samples, we developed DART-ID. This method implements a data-driven, global retention time (RT) alignment process to infer peptide RTs across experiments. DART-ID then incorporates the global RT-estimates within a principled Bayesian framework to increase the confidence in correct peptide-spectrum-matches. Applying DART-ID to hundreds of samples prepared by the Single Cell Proteomics by Mass Spectrometry (SCoPE-MS) design increased the peptide and proteome coverage by 30 - 50% at 1% FDR. The newly identified peptides and proteins were further validated by demonstrating that their quantification is consistent with the quantification of peptides identified from high-quality spectra. DART-ID can be applied to various sets of experimental designs with similar sample complexities and chromatography conditions, and is freely available online.
DOI: 10.25989/1zhq-gw65
title: Materials Experiment and Analysis Database:
DOI: 10.25989/5f02-wd08
title: Materials Experiment and Analysis Database:
DOI: 10.25989/7c1y-cn14
title: Materials Experiment and Analysis Database:
DOI: 10.25989/cfvy-6869
title: Materials Experiment and Analysis Database:
DOI: 10.25989/fgp2-cb64
title: Materials Experiment and Analysis Database:
DOI: 10.25989/ry16-0c09
title: Materials Experiment and Analysis Database:
DOI: 10.25989/tmt9-pm93
title: Materials Experiment and Analysis Database:
DOI: 10.25989/vb7b-zb14
title: Materials Experiment and Analysis Database:
DOI: 10.25345/c50w3m
title: MassIVE MSV000083158 - An iTRAQ based comparative proteomic profiling of thermotolerant Saccharomyces cerevisiae JRC6 in response to high temperature fermentation
title: To identify proteomic changes responsible for imparting thermotolerance by iTRAQ based profiling of Saccharomyces cerevisiae JRC6 by growing at optimum (30 degree C) and high temperature (40  degree C).
DOI: 10.25345/c51w2j
title: MassIVE MSV000083156 - NBOMeyjs
title: This massive data set is the group of nine NBOMe derivatives, one of dope group.
DOI: 10.25345/c55p5v
title: MassIVE MSV000083155 - Tyrosyl phosphorylation of KRAS alters switch I and II conformation and disrupts multiple phases of the GTPase cycle
title: Project contains LC-MS data from an in vitro kinase assay to assess phosphorylation of small GTPase protein K-RAS. Note: proteins used are N15 labeled.
DOI: 10.25345/c59c7r
title: MassIVE MSV000083154 - OTULIN deficiency causes LUBAC degradation, dysregulated TNF signalling, and cell death in ORAS
title: We focus on the modifier ubiquitin, a small protein that modifies other proteins in a variety of distinct ways, known as the ubiquitin code.

Ubiquitination most commonly leads to destruction of the modified protein, but can also change its activation, interactions or localisation. Much of our work aims to enable studies of ubiquitin signals.
DOI: 10.25345/c5w59q
title: MassIVE MSV000083160 - RNF5 interactome
title: Cells expressing Flag-tagged RNF5 or empty vector were incubated with the proteasome inhibitor MG132 to block protein degradation. Cell lysates were then prepared and immunoprecipitationed with anti-Flag antibody were performed, and eluates were digested with trypsin and analyzed on a Q Exactive.
DOI: 10.25345/c5x60z
title: MassIVE MSV000083157 - Nrf2 activation promotes lung cancer metastasis by blocking degradation of Bach1
title: Quantitative proteomics of mouse derived  lung adenocarcinoma cell line KP ( Kras-g12d_p53-/-) compared to an isogenic KPK (KP-sgKeap1) cell line. Cell lysates were prepared in triplicates and individually labeled with TMT reagent, combined, off-line fractionated and concatenated into 40 fractions and subsequently analyzed by LC-MS.
DOI: 10.25989/13db-zj14
title: Materials Experiment and Analysis Database:
DOI: 10.25989/9caf-qr34
title: Materials Experiment and Analysis Database:
DOI: 10.25989/aj9f-7613
title: Materials Experiment and Analysis Database:
DOI: 10.25989/j6n8-ga19
title: Materials Experiment and Analysis Database:
DOI: 10.25989/s293-ne94
title: Materials Experiment and Analysis Database:
DOI: 10.25989/tyz1-gx88
title: Materials Experiment and Analysis Database:
DOI: 10.22011/strenda_db.olwlva
title: The next generation test of new fields

description: K(+)-stimulated pyrophosphate-energized sodium pump (Membrane-bound sodium-translocating pyrophosphatase) (Pyrophosphate-energized inorganic pyrophosphatase) (Na(+)-PPase) (Tm-PPase), Q9S5X0, diphosphate + H2O = 2 phosphate
DOI: 10.22011/strenda_db.xg9ety
title: The next generation test of new fields

description: Hexokinase-2 (Hexokinase PII) (Hexokinase-B), P04807, ATP + D-hexose = ADP + D-hexose 6-phosphate
DOI: 10.25345/c5h02x
title: MassIVE MSV000083163 - Club LRP1 KO
title: Primary airway epithelial cells were isolated from WT and Club LRP1-/- mice  as in Oreffo et al. Briefly, mice were anesthetized with isofluorane and their trachea was cannulated. Abdominal cavity was opened, and heart was perfused with PBS until the lungs and liver were free of blood. The lungs were then lavaged through the tracheal cannula with 1 mL saline, followed by protease solution (0.25% crystalline trypsin in 133 mM NaCl, 5.2 mM KCl, 1.89 mM CaCl2, 1.29 mM MgSO4, 2.59 mM phosphate buffer, pH 7.4, 10.3 mM Hepes buffer , pH 7.4, glucose 1 mg/ml),  and then infused with protease solution according to the standard lung perfusion guidelines by the American Thoracic Society (61). Lungs were maintained filled with protease solution at 37 C for 15 min. Then, lungs and airways were extracted from the chest cavity and dissected in protease solution supplemented with fetal bovine serum. Trachea and major bronchi were removed and the parenchyma was diced in small pieces, placed in solution B (5.2 mM KCl, 2.59 mM phosphate buffer, pH 7.4, 10.3 mM Hepes buffer, Ph 7.4, glucose 1 mg/ml) and manually shaken to release the digested cells. The cell suspension was then filtered through gauze and 100 and 40 um mesh. The primary cell digest was centrifuged twice at 32 x g for 6 min at 10 C in 4 mL solution B with 250 ug/mL DNAse and the final pellet collected. 
Proteomic analysis. Airway epithelial cells collected as above were submitted to Bioproximity LLC (Chantilly, VA, USA). For proteome profiling, cells were trypsinized and equal amounts of protein per sample were used for UPLC-MS/MS for identification of protein IDs.
DOI: 10.25345/c5mp4h
title: MassIVE MSV000083162 - GNPS-DGP
title: The potential physiological activity of food-derived peptides
has been a hot topic in research during the last 30 years.
Among them, peptides with antihypertensive activity have
attracted much attention and, undoubtedly, is the group of
peptides with more solid evidence in human trials. Numerous
studies have focused on the identification of new antihypertensive
sequences from different sources, milk, cheese,meat, fish, and from a diversity of plants, algae, etc. Also, fungiand yeast sources have been studied, but waste products, suchas collagn, constitute an attractive source with substantial environmental and cost benefits.
DOI: 10.25345/c5rc85
title: MassIVE MSV000083161 - GNPS- Stachybotrys levisporius
title: fungos saprobio isolado do semiarido brasileiro- rede sisbiota
DOI: 10.25989/6her-kt32
title: Materials Experiment and Analysis Database:
DOI: 10.25989/b02s-1879
title: Materials Experiment and Analysis Database:
DOI: 10.25989/cnvd-1h64
title: Materials Experiment and Analysis Database:
DOI: 10.25989/j97k-z673
title: Materials Experiment and Analysis Database:
DOI: 10.25989/p81g-5e33
title: Materials Experiment and Analysis Database:
DOI: 10.25989/tpxy-zr15
title: Materials Experiment and Analysis Database:
DOI: 10.25989/x22w-7180
title: Materials Experiment and Analysis Database:
DOI: 10.25989/yf66-w261
title: Materials Experiment and Analysis Database:
DOI: 10.25345/c5f01x
title: MassIVE MSV000083167 - An acquired scaffolding function of the DNAJ-PKAc fusion enhances oncogenesis in Fibrolamellar carcinoma
title: Fibrolamellar carcinoma (FLC) is a rare liver cancer.  FLC tumors exclusively produce DNAJ-PKAc, a de novo chimeric enzyme consisting of a chaperonin-binding domain fused to the C subunit of protein kinase A.  Biochemical analyses of clinical samples reveal that a unique property of DNAJ-PKAc is the ability to recruit heat shock protein 70 (Hsp70).  This cellular chaperonin is frequently up-regulated in cancers.  Gene-editing of mouse hepatocytes generated disease-relevant AML12DNAJ-PKAc cell lines.  Drug-screening discovered Hsp70 and MEK inhibitor combinations that selectively block proliferation of AML12DNAJ-PKAc cells.  Further analyses indicate that the proto-oncogene AKAP-Lbc is upregulated in FLC and functions to cluster DNAJ-PKAc/Hsp70 sub-complexes with a RAF-MEK-ERK kinase module.  Phosphoproteomic profiling infers that DNAJ-PKAc biases the signaling landscape toward ERK activation and mobilizes other downstream kinase cascades. We propose that the oncogenic nature of DNAJ-PKAc proceeds through an acquired scaffolding function that permits recruitment of Hsp70 and stabilizes ERK signaling.
DOI: 10.25345/c5g02m
title: MassIVE MSV000083166 - Proteomics analysis of nuclear envelope, cytoplasmic membrane and nuclear contents fractions isolated from mesenchymal stem cells, adipocytes and myocytes
title: We used shotgun proteomics to analyze three subcellular fractions isolated from mesenchymal stem cells and from differentiated adipocytes and myocytes:  nuclear envelopes (NEs), cytoplasmic membranes and nuclear contents.  The proteomics data were analyzed by a NSAF-based scoring system to calculate relative protein enrichment in the NE fraction.  High NE enrichment scores were obtained for most well-characterized NE proteins.  High scores also were seen for a number of new proteins not known to be concentrated at the NE, and we validated that five of these are substantially concentrated at the NE of multiple cell types. Our datasets can be useful for identifying additional NE-concentrated proteins in the future.
DOI: 10.25345/c5kp46
title: MassIVE MSV000083165 - D vulgaris WT-IPFG07 chemostat comparison
title: Parallel chemostats of Desulfovibrio vulgaris Hildenborough WT and IPFG07 (DsrC low-expression) mutant were sampled over 5 turnovers at steady-state. Extracted proteins were digested with trypsin and peptides were isotopically labeled for quantification using the diDO-IPTL methodology (Waldbauer et al. 2017 Analytical Chemistry).
DOI: 10.25345/c5qg7h
title: MassIVE MSV000083164 - LCMS data files for PPATHOGENS-D-18-02228
title: Two data files characterizing and verifying processed, recombinant expressed forms of proteins from homo sapiens and Borreliela burdorferi
DOI: 10.25989/2va5-bj87
title: Materials Experiment and Analysis Database:
DOI: 10.25989/7f5y-s640
title: Materials Experiment and Analysis Database:
DOI: 10.25989/e2bn-kh22
title: Materials Experiment and Analysis Database:
DOI: 10.25989/vx8q-5135
title: Materials Experiment and Analysis Database:
DOI: 10.25989/w666-jr38
title: Materials Experiment and Analysis Database:
DOI: 10.25989/y1nb-bz15
title: Materials Experiment and Analysis Database:
DOI: 10.25345/c50s3k
title: MassIVE MSV000083169 - Completion of the cytosolic post-chorismate phenylalanine biosynthetic pathway in plants
title: In addition to being a vital component of proteins, phenylalanine is also a precursor of numerous aromatic primary and secondary metabolites with broad physiological functions. In plants phenylalanine is synthesized predominantly via the arogenate pathway in plastids. Here, we describe the structure, molecular players and subcellular localization of a microbial-like phenylpyruvate pathway for phenylalanine biosynthesis in plants. Using a reverse genetic approach and metabolic flux analysis, we provide evidence that the cytosolic chorismate mutase is responsible for directing carbon flux towards cytosolic phenylalanine production via the phenylpyruvate pathway. We also show that an alternative transcription start site of a known plastidial enzyme produces a functional cytosolic prephenate dehydratase that catalyzes the conversion of prephenate to phenylpyruvate, the intermediate step between chorismate mutase and phenylpyruvate aminotransferase. Thus, our results complete elucidation of phenylalanine biosynthesis via phenylpyruvate in plants, showing that this pathway splits from the known plastidial arogenate pathway at chorismate, instead of prephenate as previously thought, and the complete pathway is localized in the cytosol.
DOI: 10.25345/c54g77
title: MassIVE MSV000083168 - Chemical Derivatization of Streptavidin Provides Protection from Tryptic Proteolysis
title: A novel approach toward the protection of affinity purification matrices, such as the protein streptavidin or immunoglobulins, from tryptic digestion.  This allows for on-bead enzymatic digestion, while minimizing contamination from the affinity purification matrix.
DOI: 10.25345/c5831d
title: MassIVE MSV000083173 - GNPS Taonia atomaria fractions mode negatif (F10,F14-F28)
title: Samples :  extract of Taonia atomaria (Brown algae). Sampling site: Carqueiranne (France). nagative mode
DOI: 10.25345/c5jk57
title: MassIVE MSV000083172 - stachybotrys new
title: fungo saprobio isolado do semi arido  brasileiro, em expedicoes feitas pela rede sisbiota
DOI: 10.25345/c5v31p
title: MassIVE MSV000083171 - GNPS Food Amazon - VA samples
title: Metabolite analysis of food samples. Samples were extracted in ethanol they were preserved and transported in and analyzed using FoodOmics protocols. Data were acquired using a Bruker Daltonics maXis Impact and C18 RP-UHPLC. Positive polarity acquisition of LC-MS and LC-MS/MS.
DOI: 10.25345/c5w02b
title: MassIVE MSV000083170 - Proteomic analysis of bacterial response to a 4-hydroxybenzylidene indolinone compound, which re-sensitizes bacteria to traditional antibiotics
title: Halogenated 4-hydroxybenzylidene indolinones have been shown to re-sensitize methicillin-resistant S. aureus (MRSA) and vancomycin-resistant E. faecalis (VRE) to methicillin and vancomycin respectively. The mechanism of antibiotic re-sensitization was however not previously studied. Here, we present the global proteomics analysis of S. aureus treated with GW5074, a 4-hydroxybenzylidene indolinone compound. Global proteomics analysis revealed that GW5074 treatment resulted in the downregulation of AgrC (a quorum sensing-related histidine kinase), AgrA (a quorum sensing-related response regulator) as well as downstream targets, such as hemolysins, lipases and proteases in S. aureus. Significant downregulation of enzymes involved in the purine biosynthesis was also observed. S. aureus proteins involved in amino acid metabolism and peptide transport were observed to be downregulated. The most upregulated protein was the lytic transglycosylase, SceD. These findings shed insights into how 4-hydroxybenzylidene indolinones kill bacteria and also re-sensitize MRSA to other antibiotics.
DOI: 10.25989/0tp5-aw31
title: Materials Experiment and Analysis Database:
DOI: 10.25989/6wst-rc54
title: Materials Experiment and Analysis Database:
DOI: 10.25989/8zma-ws68
title: Materials Experiment and Analysis Database:
DOI: 10.25989/by6b-cv37
title: Materials Experiment and Analysis Database:
DOI: 10.25989/kd8r-xm80
title: Materials Experiment and Analysis Database:
DOI: 10.25989/ks1t-6848
title: Materials Experiment and Analysis Database:
DOI: 10.25989/mn7d-me30
title: Materials Experiment and Analysis Database:
DOI: 10.25989/rdd5-a395
title: Materials Experiment and Analysis Database:
DOI: 10.25989/smy9-g066
title: Materials Experiment and Analysis Database:
DOI: 10.25989/zjtx-ts12
title: Materials Experiment and Analysis Database:
DOI: 10.25345/c50k6n
title: MassIVE MSV000083175 - PU1 interactome in human monocyte derived dendritic cells
title: Human monocyte-derived DC were cultured at a density of 0.5x10E6 cells/ml in RPMI-1640 supplemented with 10% FCS, 1% Pen/Strep, 10 ng/ml GM-CSF and 10 ng/ml IL4. At day 7, they were stimulated or not with 500 ng/ml LPS. Cells were collected at day 10.
Whole cell lystaes from 2x10E8 cells were used for immunoprecipiation with PU.1 (T-21 SantaCruz) antibody. IgG was used as control.