PeptideAtlas Builds – Bulk Downloads

PeptideAtlas builds are performed for individual organisms and important sample groups (e.g., plasma/serum). The data products of these individual builds may accessed interactively in the database via the Stats & Lists page or with custom queries, or they may be downloaded in their entirety below.

Each build has a peptide inclusion cutoff criterion. A build with a cutoff of "P≥0.9" is a build in which only peptides with a PeptideProphet probability of at least 0.9 are included. A build with a PSM FDR (false discovery rate) threshold usually denotes a build with a protein FDR of 1%. For these builds, a peptide usually must have a probability much greater than 0.9 to be included.

For builds with P≥0.9 cutoffs, PSMs and peptides are counted only for multiply observed peptides; singletons are omitted because these identifications are quite unreliable at this generous cutoff.