PXD000154

PXD000154 is an original dataset announced via ProteomeXchange.

Title	MSe_Bsubtilis168
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	2014-08-04
AnnouncementXML	Submission_2014-08-04_05:49:33.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sandra Maass
SpeciesList	scientific name: Bacillus subtilis (strain 168); NCBI TaxID: 224308;
ModificationList	deamidated residue; monohydroxylated residue; iodoacetamide derivatized residue; 2-pyrrolidone-5-carboxylic acid (Gln)
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

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]

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

Sandra Maass
contact affiliation	Department of Microbial Physiology
contact email	sandra.maass@uni-greifswald.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/08/PXD000154

PRIDE project URI

• PRIDE
  1. PXD000154
     1. Label: PRIDE project
     2. Name: MSe_Bsubtilis168