Dataset Information

Comprehensive Absolute Quantification of the Cytosolic Proteome of Bacillus subtilis by Data Independent, Parallel Fragmentation in Liquid Chromatography/Mass Spectrometry (LC/MS)

ABSTRACT: 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).

INSTRUMENT(S):

ORGANISM(S): Bacillus Subtilis Subsp. Subtilis Str. 168

SUBMITTER: Sandra Maass

LAB HEAD: Sandra Maass

PROVIDER: PXD000154 | Pride | 2014-08-04

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	RAW_MSe_Bsubtilis168_CH_Bio1_1.zip	Other
	RAW_MSe_Bsubtilis168_CH_Bio1_2.zip	Other
	RAW_MSe_Bsubtilis168_CH_Bio1_3.zip	Other
	RAW_MSe_Bsubtilis168_CH_Bio2_1.zip	Other
	RAW_MSe_Bsubtilis168_CH_Bio2_2.zip	Other

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Publications

Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E)).

Muntel Jan J Fromion Vincent V Goelzer Anne A Maaβ Sandra S Mäder Ulrike U Büttner Knut K Hecker Michael M Becher Dörte D

Molecular & cellular proteomics : MCP 20140131 4

In the growing field of systems biology, the knowledge of protein concentrations is highly required to truly understand metabolic and adaptational networks within the cells. Therefore we established a workflow relying on long chromatographic separation and mass spectrometric analysis by data independent, parallel fragmentation of all precursor ions at the same time (LC/MS(E)). By prevention of discrimination of co-eluting low and high abundant peptides a high average sequence coverage of 40% cou ...[more]

PMID: 24696501

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