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Multi-center study of E.coli colonies as a proof of concept for federated proteomics.

ABSTRACT: Quantitative mass spectrometry has transformed proteomics by allowing the simultaneous quantification of thousands of proteins. To boost statistical power, it is necessary to increase sample sizes by combining patient-derived data from various institutions. However, this practice raises significant privacy concerns. We created a DIA-LFQ dataset containing 118 samples generated from Escherichia coli MG1655 (DSM 18039) cultures and distributed them to five independent proteomics centers. This distributed data were used as a proof of concept to introduce FedProt - the first privacy-preserving tool for collaborative differential protein abundance analysis of distributed data.

INSTRUMENT(S):

ORGANISM(S): Escherichia Coli

SUBMITTER: Yuliya Burankova

LAB HEAD: Prof. Dr. Jan Baumbach

PROVIDER: PXD053812 | Pride | 2025-04-29

REPOSITORIES: Pride

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			Action	DRS
	20230516_EXPL1_LiSc_SA_S610_RT_25_s2.raw	Raw
	20230516_EXPL1_LiSc_SA_S610_RT_26_s9.raw	Raw
	20230516_EXPL1_LiSc_SA_S610_RT_27_s12.raw	Raw
	20230516_EXPL1_LiSc_SA_S610_RT_28_s17.raw	Raw
	20230516_EXPL1_LiSc_SA_S610_RT_29_s24.raw	Raw

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Project 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.

Dataset Information

Multi-center study of E.coli colonies as a proof of concept for federated proteomics.

Dataset's files

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