34	datasets
61	experiments
1,811	MS runs
36,339,335	PSMs
1,767,878	distinct peptides
10,673	canonical proteins

About

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

Available datasets of Drosophila 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

A high-quality catalog of the Drosophila melanogaster proteome
Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R
Nat Biotechnol. 2007 May;25(5):576-83
DOI : 10.1038/nbt1300. Epub 2007 Apr 22. PMID: 17450130

Download

Below are individual Drosophila 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.

Drosophila 2026-04 PSM FDR = 0.0005Latest Build

Biosequence Set in FASTA format [80MB]
Database tables exported as TSV dump file [258MB]
Database tables exported as mysql dump file [229MB]
Peptide CDS and chromosomal coordinates [370MB]
Peptide CDS coordinates [211MB]
Peptide sequences in FASTA format [15MB]

Drosophila 2012-08 PSM FDR = 0.00001

Biosequence Set in FASTA format [73MB]
Database tables exported as an XML file [27MB]
Database tables exported as mysql dump file [15MB]
Peptide CDS and chromosomal coordinates [26MB]
Peptide CDS coordinates [13MB]
Peptide sequences in FASTA format [1MB]

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Drosophila 2011-09 PSM FDR = 0.001

Biosequence Set in FASTA format [26MB]
Database tables exported as an XML file [26MB]
Database tables exported as mysql dump file [15MB]
Peptide CDS and chromosomal coordinates [17MB]
Peptide CDS coordinates [9MB]
Peptide sequences in FASTA format [1MB]

Drosophila 2010-06 PSM FDR = 0.001

Biosequence Set in FASTA format [26MB]
Database tables exported as an XML file [96MB]
Database tables exported as mysql dump file [58MB]
Peptide CDS and chromosomal coordinates [16MB]
Peptide CDS coordinates [8MB]
Peptide sequences in FASTA format [1MB]

Drosophila 2009-07 P >= 0.9

Biosequence Set in FASTA format [25MB]
Database tables exported as an XML file [30MB]
Database tables exported as mysql dump file [18MB]
Peptide CDS and chromosomal coordinates [15MB]
Peptide CDS coordinates [7MB]
Peptide sequences in FASTA format [1MB]

Help

Complete description of each of the available download formats