40	datasets
116	experiments
1,062	MS runs
23,823,673	PSMs
537,885	distinct peptides
3,509	canonical proteins

About

The Escherichia coli PeptideAtlas provides a compendium of results from uniformly reprocessed mass spectrometry proteomics datasets.

Available datasets of Escherichia coli were reprocessed from MS raw files using the Trans-Proteomic Pipeline suite of tools.

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All detected Escherichia coli proteins

Publications

The E. coli PeptideAtlas Build: Characterizing the observed Escherichia coli pan-proteome and its post-translational modifications; Caroline Jachmann, Zhi Sun, Kevin Velghe, Florence Arsène-Ploetze, Aurélie Hirschler, Jasper Zuallaert, Christine Carapito, Robbin Bouwmeester, Kay Nieselt, Eric Deutsch, Lennart Martens, Ralf Gabriels, Tim Van Den Bossche
[ bioRxiv preprint ]

Download

Below are individual Escherichia coli PeptideAtlas builds available for download in various flat file formats. Note that not all files contain all information from the build. A build subtitled "PSM FDR=0.002" denotes a PSM FDR threshold of 0.002 (0.2%) is applied to every sample in the build.

Escherichia coli 2024-11 PSM FDR = 0.0002Latest Build

Biosequence Set in FASTA format [30MB]
Database tables exported as TSV dump file [91MB]
Database tables exported as mysql dump file [75MB]
Peptide CDS and chromosomal coordinates [94MB]
Peptide CDS coordinates [62MB]
Peptide sequences in FASTA format [4MB]

Escherichia coli 2024-02 PSM FDR = 0.00026

Biosequence Set in FASTA format [3MB]
Peptide CDS and chromosomal coordinates [3MB]
Peptide CDS coordinates [2MB]
Peptide sequences in FASTA format [1MB]

Help

Complete description of each of the available download formats

Other Resources

Escherichia coli K-12 substr. MG1655 database at EcoCyc
E coli Phosophoproteome PeptideAtlas
Previous E coli PeptideAtlas builds: [ 2024-02 ]