37	datasets
81	experiments
1,584	MS runs
22,055,712	PSMs
410,033	distinct peptides
9,275	canonical proteins

About

The C. elegans PeptideAtlas provides a compendium of results from uniformly reprocessed mass spectrometry proteomics datasets.

Available datasets of Caenorhabditis elegans samples were reprocessed from the raw files using the Trans-Proteomic Pipeline suite of tools.

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All detected canonical proteins

Chromosome Summary

Column descriptions ▲

Entries: Number of entries in each chromosome
Canonical: Proteins seen with 2 distinct, uniquely mapping peptides
Uncertain: Proteins with some evidence that is not sufficient for canonical status
Redundant: Proteins that have peptides that map to them, but not uniquely and thus not needed to explain the observed peptides
Not Observed: No detections at all in PeptideAtlas above our very stringent threshold

Publications

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes
Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, et al. (2009)
PLOS Biology 7(3): e1000048
DOI: 10.1371/journal.pbio.1000048

Download

Below are individual C. elegans 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.

C. elegans 2026-05 PSM FDR = 0.001Latest Build

Biosequence Set in FASTA format [68MB]
Database tables exported as TSV dump file [197MB]
Database tables exported as mysql dump file [178MB]
Peptide CDS and chromosomal coordinates [201MB]
Peptide CDS coordinates [111MB]
Peptide sequences in FASTA format [11MB]

C. elegans 2016-06 PSM FDR = 0.00001

Biosequence Set in FASTA format [51MB]
Peptide CDS and chromosomal coordinates [52MB]
Peptide CDS coordinates [34MB]
Peptide sequences in FASTA format [4MB]

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C. elegans 2013-09 PSM FDR = 0.00035

Biosequence Set in FASTA format [43MB]
Database tables exported as an XML file [49MB]
Database tables exported as mysql dump file [27MB]
Peptide CDS and chromosomal coordinates [25MB]
Peptide CDS coordinates [16MB]
Peptide sequences in FASTA format [3MB]

C. elegans 2011-08 Ens62 PSM FDR = 0.0025

Biosequence Set in FASTA format [32MB]
Database tables exported as an XML file [34MB]
Database tables exported as mysql dump file [19MB]
Peptide CDS and chromosomal coordinates [13MB]
Peptide CDS coordinates [8MB]
Peptide sequences in FASTA format [2MB]

C. elegans 2009-03 P >= 0.9

Biosequence Set in FASTA format [28MB]
Database tables exported as an XML file [39MB]
Database tables exported as mysql dump file [24MB]
Peptide CDS and chromosomal coordinates [15MB]
Peptide CDS coordinates [8MB]
Peptide sequences in FASTA format [2MB]

Help

Complete description of each of the available download formats