Direct mapping of peptide-spectral-matches to genome information facilitates qualifying proteomics information

ABSTRACT: The data set consist of three different sources. 1) All files with ecoli_* derive from a pure culture of Escherichia coli K-12 (MG1655). 2) All files with SIHUMI_standard_* derive from a mixed culture of 8 bacteria (SIHUMIx) Anaerostipes caccae (DSMZ 14662), Bacteroides thetaiotaomicron (DSMZ 2079), Bifidobacterium longum (NCC 2705), Blautia producta (DSMZ 2950), Clostridium butyricum (DSMZ 10702), Clostridium ramosum (DSMZ 1402), Escherichia coli K-12 (MG1655) and Lactobacillus plantarum (DSMZ 20174). A standard proteomic protocol was used for purification. 3) All files with SIHUMI_small_* derive from the same bacteria culture as second source in contrast a variety of different proteomic protocols were used to enhance enrichment of small (<100 AS) Proteins. The goal of the project was to design a workflow to quickly prioritize novel protein candidates. The workflow was designed to be robust in a meta-omics context and facilitate the integration of transcriptomic and other information on a genomic level. The MS-data from the first source was used to test the workflow under well controlled conditions, namely in pure culture and near complete annotation. The workflow was used with data from the second source to see if good results can be produced in a mixed culture. To enhance the chances of finding novel proteins we incorporated the data from the third source.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Erysipelatoclostridium Ramosum Dsm 1402 Blautia Producta Atcc 27340 = Dsm 2950 Clostridium Butyricum Dsm 10702 Anaerostipes Caccae Dsm 14662 Bifidobacterium Longum Ncc2705 Lactobacillus Plantarum Subsp. Plantarum Atcc 14917 = Jcm 1149 = Cgmcc 1.2437 Escherichia Coli Str. K-12 Substr. Mg1655 Bacteroides Thetaiotaomicron (strain Atcc 29148 / Dsm 2079 / Nctc 10582 / E50 / Vpi-5482)

TISSUE(S): Cell In Vitro

SUBMITTER: John Anders  

LAB HEAD: Prof. Dr. Martin von Bergen

PROVIDER: PXD023243 | Pride | 2021-09-09

REPOSITORIES: Pride