PXD023243

PXD023243 is an original dataset announced via ProteomeXchange.

Title	Direct mapping of peptide-spectral-matches to genome information facilitates qualifying proteomics information
Description	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.
HostingRepository	PRIDE
AnnounceDate	2021-09-10
AnnouncementXML	Submission_2021-09-09_19:39:53.735.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	John Anders
SpeciesList	scientific name: Erysipelatoclostridium ramosum DSM 1402; NCBI TaxID: 445974; scientific name: Anaerostipes caccae DSM 14662; NCBI TaxID: 411490; scientific name: Bifidobacterium longum NCC2705; NCBI TaxID: 206672; scientific name: Blautia producta ATCC 27340 DSM 2950; NCBI TaxID: 1121114; scientific name: Clostridium butyricum DSM 10702; NCBI TaxID: 1316931; scientific name: Escherichia coli str K12 substr MG1655; NCBI TaxID: 511145; scientific name: Bacteroides thetaiotaomicron VPI5482; NCBI TaxID: 226186; scientific name: Lactobacillus plantarum subsp plantarum ATCC 14917 JCM 1149 CGMCC 12437; NCBI TaxID: 525338;
ModificationList	methionine oxidation with neutral loss of 80 Da
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-21 02:38:12	ID requested
⏵ 1	2021-09-09 19:39:54	announced

Anders J, Petruschke H, Jehmlich N, Haange SB, von Bergen M, Stadler PF, A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations. BMC Bioinformatics, 22(1):277(2021) [pubmed]

submitter keyword: SIHUMI, proteome, metaomics, intestine

Prof. Dr. Martin von Bergen
contact affiliation	Helmholtz-Zentrum für Umweltforschung, Department of Molecular Systems Biology
contact email	martin.vonbergen@ufz.de
lab head
John Anders
contact affiliation	Bioinformartics Leipzig
contact email	john@bioinf.uni-leipzig.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/2021/09/PXD023243

PRIDE project URI

• PRIDE
  1. PXD023243
     1. Label: PRIDE project
     2. Name: Direct mapping of peptide-spectral-matches to genome information facilitates qualifying proteomics information