PXD058808

PXD058808 is an original dataset announced via ProteomeXchange.

Title	Proteomes of E. coli W3110 samples grown in different growth media
Description	This dataset contains E. coli W3110 samples grown in different growth conditions and harvested at different growth stages. A mapping between conditions and files is contained in the SDRF. This dataset is one of 40 projects included in the E. coli PanProteome PeptideAtlas build: Escherichia coli is a widely used model organism in molecular biology. Despite its pivotal role, a comprehensive proteome resource covering the E. coli pan-proteome and its post-translational modifications (PTMs) has been lacking. Here we present the E. coli PeptideAtlas build, the first comprehensive pan-proteome analysis of E. coli, generated from 40 high-quality public and in-house datasets spanning a broad diversity of strains, sample types, and experimental conditions, and comprising over 73 million MS/MS spectra. All datasets were reprocessed using both a closed search (Trans-Proteomic Pipeline using MSFragger) and an open search (ionbot). The E. coli PeptideAtlas build provides evidence for 4,755 proteins, including 1,410 previously lacking protein-level support in UniProt. The resource offers protein coverage, modification sites, raw spectra with matched peptides, and manually annotated metadata for the E. coli pan proteome. PTM profiling identified over 10,000 modification sites, including phosphorylation (3,806), acetylation (754), methylation (730), glutathionylation (352) and phosphoribosylation (226). Analysis of the glutathionylation sites revealed potential links to metal binding regulation. We also detected proteins likely associated with phages, underscoring the value of pan-proteomic approaches for studying host-phage interactions. All identifications are publicly accessible and traceable through the PeptideAtlas interface. We expect that the E. coli PeptideAtlas build will provide a useful resource for the community, which supports, for example, targeted MS experiment design, PTM enrichment method development, and strain typing. It allows straightforward lookups of protein and peptide identifications and facilitates comparative proteomic analyses by enabling the assessment of protein presence and variability across different E. coli strains. The build is available at https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=585.
HostingRepository	PRIDE
AnnounceDate	2025-09-18
AnnouncementXML	Submission_2025-09-18_05:24:18.010.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Caroline Jachmann
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-12 02:29:32	ID requested
⏵ 1	2025-09-18 05:24:18	announced

Dataset with its publication pending

submitter keyword: growth medium, growth phase,E.coli, LC-MS/MS

Christine Carapito
contact affiliation	Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, Strasbourg, France
contact email	ccarapito@unistra.fr
lab head
Caroline Jachmann
contact affiliation	1) VIB-UGent Center for Medical Biotechnology, VIB, Suzanne Tassierstraat 1, 9052 Belgium 2) Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052, Belgium
contact email	caroline.jachmann@ugent.be
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/2025/09/PXD058808

PRIDE project URI

• PRIDE
  1. PXD058808
     1. Label: PRIDE project
     2. Name: Proteomes of E. coli W3110 samples grown in different growth media