DOI: 10.5061/dryad.2z34tmpxj
title: Mass spectrometry-based proteomics of the Aurantiochytrium limacinum ATCC MYA-1381 zoospore-to-vegetative cell transition (MaxQuant processed data)

description: This dataset provides standard MaxQuant proteomic output files generated
 from an analysis of the Aurantiochytrium limacinum ATCC MYA-1381
 zoospore-to-vegetative cell transition. Mass spectrometry data from three
 biological time-course replicates were analyzed using two separate protein
 prediction sets: one from a JGI genome annotation and the other from the
 Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)
 annotation of the A. limacinum proteome. Each biological replicate in the
 dataset includes protein abundance measurements across five time points,
 capturing dynamic proteomic changes associated with cellular remodeling,
 metabolism, and ectoplasmic network formation. Data is provided as
 outputted from MaxQuant, including quantitative values for protein group
 identification and peptide-level measurements.
description: <em>Aurantiochytrium limacinum</em> ATCC MYA-1381 was
 cultured at 25°C in GPY medium containing 3% D-glucose, 1.5% peptone, 0.5%
 yeast extract, and 1.8% Instant Ocean sea salt. After 24 hours, cells were
 transferred to GPY agar plates and grown for an additional 24 hours.
 Zoospores were released by flooding plates with artificial seawater (1.8%
 Instant Ocean) and collected after 2 hours. Zoospores were inoculated into
 petri dishes containing A1 medium, and samples were collected at five time
 points: zoospores at 0 hours (T0) and settled cells at 2, 4, 6, and 8
 hours post-settlement (T2, T4, T6, T8). Cells were harvested by
 centrifugation, and pellets were stored at -80°C for protein
 extraction. Protein extraction was performed using a
 lysis buffer containing KCl, MgCl₂, Tris, NP-40, Tween, SDS, and deionized
 water. Samples were vortexed, centrifuged, and supernatants were
 collected. Protein concentration was determined using a bicinchoninic acid
 (BCA) assay. Proteins were digested with trypsin and labeled using
 iTRAQ-8plex reagents (113–117). Peptides were fractionated by
 high-performance liquid chromatography (HPLC) and analyzed using an
 Ultimate 3000 nano UHPLC system coupled to a Q Exactive mass spectrometer
 (Thermo Fisher Scientific). Mass spectrometry data were
 analyzed separately against two predicted A. limacinum proteomes: one from
 the JGI genome annotation (MycoCosm) and the other from the Marine
 Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) annotation.
 Searches were conducted using MaxQuant v1.6.2.14 with trypsin enzyme
 specificity allowing up to two missed cleavages. Carbamidomethylation of
 cysteine was set as a fixed modification, while oxidation of methionine
 and iTRAQ-8plex labeling were included as variable modifications. The
 precursor mass tolerance was set to 10 ppm, and the MS/MS tolerance was
 0.6 Da. MaxQuant output included standard protein identification and
 quantification metrics, with results organized into per-replicate
 proteinGroups and peptides, as well as summary tables of total reporter
 intensities and normalized (corrected) values.
description: # Mass spectrometry-based proteomics of the Aurantiochytrium limacinum
 ATCC MYA-1381 zoospore-to-vegetative cell transition (MaxQuant processed
 data) ## **Dataset Overview** This dataset contains proteomic data from an
 analysis of the *Aurantiochytrium limacinum* ATCC MYA-1381
 zoospore-to-vegetative cell transition. Mass spectrometry data from three
 biological replicates were processed using MaxQuant and analyzed
 separately against two different protein prediction sets: JGI genome
 annotation (MycoCosm), and Marine Microbial Eukaryote Transcriptome
 Sequencing Project (MMETSP) annotation. Each dataset includes protein
 abundance measurements across five time points (T0, T2, T4, T6, T8),
 capturing proteomic changes associated with cellular remodeling,
 metabolism, and ectoplasmic network formation. ## **Contents of the
 Dataset** The dataset consists of two main spreadsheet files corresponding
 to the two protein prediction sets used in MaxQuant analysis: *
 **JGI_maxquant.xlsx** * **MMETSP_maxquant.xlsx** Each file contains
 multiple tabs corresponding to standard MaxQuant output: *
 **proteinGroups_G1, G2, G3**: Protein-level identification and
 quantification tables for each biological replicate. * **peptides_G1, G2,
 G3**: Peptide-level identification and quantification tables for each
 replicate. * **Reporter_intensity_raw**: Unnormalized reporter ion
 intensities across timepoints and replicates, aggregated per protein
 group. * **Reporter_intensity_corrected**: Normalized reporter ion
 intensities, rescaled per channel to account for variation in labeling or
 loading. ### **ProteinGroups Tabs
 (`proteinGroups_G1`,`proteinGroups_G2`,`proteinGroups_G3`)** Each row
 represents a protein group detected in the sample. Selected columns
 include: * **Protein IDs**: Accession identifiers for the proteins in this
 group. * **Majority protein IDs**: The most representative protein for the
 group (used for annotation). * **Peptide counts**: Various counts of
 peptides detected (all / razor+unique / unique). * **Fasta headers**:
 Original FASTA header from the input proteome. * **Sequence coverage**:
 Percentage of protein sequence covered by identified peptides. * **Mol.
 weight [kDa]**: Molecular weight of the majority protein. * **Q-value**:
 False discovery rate-adjusted confidence score. * **Reporter intensity
 113–117**: Raw reporter ion intensities for each iTRAQ label.\ (*Note: The
 `Reporter intensity corrected` columns are present but identical and
 unmodified.*) * **Intensity**: Summed intensity across channels. * **MS/MS
 count**: Number of fragment spectra supporting the identification. *
 **Reverse / Potential contaminant**: Flags for decoy hits or common
 contaminants (`+` if true). * **Oxidation (M) site positions**:
 Position(s) of methionine oxidation modifications if detected. ###
 **Peptides Tabs (`peptides_G1`, `peptides_G2`,`peptides_G3`)** Each row
 represents a unique peptide identified in the sample. * **Sequence**:
 Amino acid sequence of the peptide. * **Amino acid Count**: Count of each
 residue type . * **Missed cleavages**: Missed tryptic cleavage sites
 (integer). * **Mass**: Monoisotopic mass of the peptide. * **PEP**:
 Posterior error probability of the identification. * **Reporter intensity
 113–117**: Raw reporter ion intensities for each iTRAQ label.\ (*The
 `Reporter intensity corrected` columns are present but identical and
 unmodified.*) * **Mod. peptide IDs**: ID for the modified form of the
 peptide. * **Reverse / Potential contaminant**: Identification flags. ###
 Reporter\_intensity\_raw and Reporter\_intensity\_corrected Tabs These two
 tabs summarize reporter ion intensities for timepoints and replicates,
 aggregated per protein group. * **Reporter_intensity_raw**: Contains the
 unnormalized reporter ion intensities (`Reporter intensity` values from
 MaxQuant), organized by protein group and experimental condition. *
 **Reporter_intensity_corrected**: Contains normalized reporter ion
 intensities, in which each iTRAQ channel was rescaled by a single
 multiplicative factor to correct for variation in sample loading or
 labeling efficiency. One channel served as the normalization reference and
 was not scaled. In both tabs, columns follow the format: **Reporter
 intensity [Channel]_[Replicate]_T[Timepoint]**\ For example: * `Reporter
 intensity 113_G1_T0-1` = iTRAQ channel 113, biological replicate [G]1,
 timepoint T0, biological replicate 1 Each row represents a protein group,
 with intensities reflecting the summed reporter signal across all peptides
 assigned to that group. ### **Missing or Empty Values** Some columns in
 the dataset contain empty cells. These are retained in their original
 MaxQuant format and are not errors or omissions. Instead, they reflect
 values that are either **not applicable** to a particular entry or were
 **not identified in the experiment**. Below is a summary of common cases:
 * **`Only identified by site` (proteinGroups)**: Empty unless a protein
 group is identified solely by a modified peptide (and not a peptide
 sequence). Most entries are fully identified and leave this field blank. *
 **`Reverse` / `Potential contaminant` (proteinGroups and peptides)**:
 These fields are part of MaxQuant’s internal false discovery rate and
 contaminant checking system. Most valid protein or peptide entries are not
 reverse hits or contaminants, and thus these cells are empty. *
 **`Oxidation (M) site IDs` / `Oxidation (M) site positions`**: These
 fields are populated only if oxidation of methionine residues was observed
 for a particular peptide or protein group. If no oxidation is detected,
 the field is left blank. * **`Taxonomy IDs`**: This column is part of
 MaxQuant's support for multi-species analyses. As this dataset only
 includes *Aurantiochytrium limacinum*, taxonomy IDs are not populated and
 the field remains empty. We chose to retain the original MaxQuant output
 format to ensure compatibility with standard proteomics pipelines. If a
 cell is empty, it indicates either a missing value (i.e., not observed or
 applicable) or a feature not detected in the sample. ### **Units and
 Values** * **Intensity values**: Arbitrary units derived from MS signal;
 useful for relative quantification. * **Q-values / PEP**: Range from 0 to
 1; lower values reflect higher confidence. * **Sequence coverage [%]**:
 Range from 0 to 100. * **Mass / Molecular weight**: Measured in Daltons
 (Da) or kiloDaltons (kDa). ### **Additional Notes** * All quantification
 values are channel-based and reflect the iTRAQ 8-plex design: * **113** =
 T0 * **114** = T2 * **115** = T4 * **116** = T6 * **117** = T8 Each
 replicate has its own set of these channels. ### **Abbreviations and
 Codes** * **T0, T2, T4, T6, T8** – Time points representing 0, 2, 4, 6,
 and 8 hours post-settlement. * **JGI** – Joint Genome Institute
 annotation. * **MMETSP** – Marine Microbial Eukaryote Transcriptome
 Sequencing Project annotation. ## **References** * For full descriptions
 of columns and analysis parameters, please refer to: * MaxQuant
 documentation: [https://www.maxquant.org/](https://www.maxquant.org/) *
 Cox & Mann, 2008. *Nature Biotechnology*, [DOI:
 10.1038/nbt.1511](https://doi.org/10.1038/nbt.1511) * Tyanova et al.,
 2016. *Nature Protocols*, [DOI:
 10.1038/nprot.2016.136](https://doi.org/10.1038/nprot.2016.136) ##
 **Software Requirements** To open and analyze the dataset, the following
 software is recommended: * **DEP v1.20.0** (Bioconductor package) for
 processing MaxQuant output, normalization, and statistical analysis *
 Available at:
 [https://bioconductor.org/packages/release/bioc/html/DEP.html](https://bioconductor.org/packages/release/bioc/html/DEP.html) * **Perseus** , optionally, for further statistical analysis of MaxQuant output * Available at: [https://maxquant.net/perseus](https://maxquant.net/perseus) * **Spreadsheet software** (e.g., Microsoft Excel, Google Sheets, or LibreOffice) for viewing `.xlsx` files ## **Contact Information** For any questions regarding this dataset, please contact: Jackie Collier; [jackie.collier@stonybrook.edu](mailto:jackie.collier@stonybrook.edu) or Joshua Rest; [joshua.rest@stonybrook.edu](mailto:joshua.rest@stonybrook.edu)