The Escherichia coli PeptideAtlas Build: Characterizing the Observed Escherichia coli Pan-Proteome and Its Post-Translational Modifications

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 data sets spanning a broad diversity of strains,
sample types, and experimental conditions, and comprising over 73
million MS/MS spectra. All data sets 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 4755 proteins, including 1376 previously
lacking protein-level support in UniProtKB. 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 (3806), 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 stemming from 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://peptideatlas.org/builds/ecoli/.