PXD000154

PXD000154 is an original dataset announced via ProteomeXchange.

Title	Comprehensive Absolute Quantification of the Cytosolic Proteome of Bacillus subtilis by Data Independent, Parallel Fragmentation in Liquid Chromatography/Mass Spectrometry (LC/MS)
Description	Absolute protein quantification for cytosolic proteins of B. subtilis growing on a carbon source (condition S) or on an amino acid source (condition CH). Data for 3 biological replicates and 3 technical replicates each for each condition are provided. For data processing and protein identification, raw data were imported into ProteinLynx Global Server 2.4(PLGS, Waters) and processed via Apex3D algorithm with following parameters:chromatographic peak width:automatic, MS ToF resolution: automatic, lock mass for charge 2:785.8426Da/e, lock mass window: 0.25Da, low energy threshold: 250cts, elevated energy threshold: 30cts, retention time window: automatic, intensity threshold of precursor/fragment ion cluster:1000cts. Database search was carried out by the ion accounting algorithm against randomized _B. subtilis_ 168 database with added common laboratory contaminants and yeast ADH1 sequence (8,438 entries) using following parameters: peptide tolerance:automatic, protein tolerance: automatic, min fragment ions matches per peptide: 1, min fragment ions matches per protein: 5, min peptide matches per protein: 2, primary digest reagent: trypsin, missed cleavages: 2, variable modifications: carbamidomethylation C (+57.0215), deamidation N, Q (+0.9840),oxidation M (+15.9949), pyrrolidonecarboxylacid N-TERM (-27.9949), false discovery rate (FDR): 5%, calibration protein: yeast ADH1. With PLGS absolute protein quantification is based on comparison of the summed signal intensities of the three most intense peptides of a protein to these of ADH1 (Hi3 approach).
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:18:50.934.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sandra Maass
SpeciesList	scientific name: Bacillus subtilis subsp. subtilis str. 168; NCBI TaxID: 224308;
ModificationList	2-pyrrolidone-5-carboxylic acid (Gln); monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2013-02-20 04:19:06	ID requested
1	2014-08-04 05:49:34	announced
⏵ 2	2024-10-22 04:18:51	announced	2024-10-22: Updated project metadata.

10.1074/mcp.M113.032631;

Muntel J, Fromion V, Goelzer A, Maa, β S, M, ä, der U, B, ü, ttner K, Hecker M, Becher D, Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E)). Mol Cell Proteomics, 13(4):1008-19(2014) [pubmed]

curator keyword: Biological

submitter keyword: absolute protein quantification, MSe, Synapt (Waters),DIA, B. subtilis

Sandra Maass
contact affiliation	University of Greifswald, Department for Microbial Proteomics
contact email	sandra.maass@uni-greifswald.de
lab head
Sandra Maass
contact affiliation	University of Greifswald, Department for Microbial Proteomics
contact email	sandra.maass@uni-greifswald.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000154
     1. Label: PRIDE project
     2. Name: Comprehensive Absolute Quantification of the Cytosolic Proteome of Bacillus subtilis by Data Independent, Parallel Fragmentation in Liquid Chromatography/Mass Spectrometry (LC/MS)