33	datasets
37	experiments
1,019	MS runs
38,745,747	spectra searched
7,296,153	PSMs
4,944	canonical proteins

About

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

Available datasets of mus musculus blood plasma samples were reprocessed from the raw files using the Trans-Proteomic Pipeline suite of tools.

Explore

form...

BROWSE

All detected Mouse 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

Download

Below are individual Mouse Plasma 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.

Mouse Plasma 2026-10 PSM FDR = 0.0005Latest Build

Biosequence Set in FASTA format [202MB]
Database tables exported as TSV dump file [67MB]
Database tables exported as mysql dump file [67MB]
Peptide CDS and chromosomal coordinates [102MB]
Peptide CDS coordinates [54MB]
Peptide sequences in FASTA format [3MB]

Mouse Plasma 2023-04 PSM FDR = 0.0005

Biosequence Set in FASTA format [201MB]
Database tables exported as TSV dump file [41MB]
Database tables exported as mysql dump file [41MB]
Peptide CDS and chromosomal coordinates [57MB]
Peptide CDS coordinates [30MB]
Peptide sequences in FASTA format [2MB]

View Older Downloads ▲

Mouse Plasma 2012-09 PSM FDR = 0.00006

Biosequence Set in FASTA format [152MB]
Database tables exported as an XML file [4MB]
Database tables exported as mysql dump file [2MB]
Peptide CDS and chromosomal coordinates [4MB]
Peptide CDS coordinates [2MB]
Peptide sequences in FASTA format [231KB]

Mouse Plasma 2011-09 PSM FDR = 0.00006

Biosequence Set in FASTA format [109MB]
Database tables exported as an XML file [4MB]
Database tables exported as mysql dump file [2MB]
Peptide CDS and chromosomal coordinates [4MB]
Peptide CDS coordinates [2MB]
Peptide sequences in FASTA format [231KB]

Mouse Plasma 2010-06 PSM FDR = 0.0001

Biosequence Set in FASTA format [105MB]
Database tables exported as an XML file [180MB]
Database tables exported as mysql dump file [112MB]
Peptide CDS and chromosomal coordinates [3MB]
Peptide CDS coordinates [1MB]
Peptide sequences in FASTA format [205KB]

Mouse Plasma 2007-05 Protein Prob >= 0.9

Biosequence Set in FASTA format [399KB]
Database tables exported as an XML file [14MB]
Database tables exported as mysql dump file [11MB]

Help

Complete description of each of the available download formats