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Full 2022-12 Build Summary
874MS runs
30,909,699searched spectra
704,426distinct peptides
11,352canonical proteins


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

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


SEARCH(e.g. Os05t0144400-01)


A publication describing the Rice PeptideAtlas build is in progress. For now, please just reference this URL, and check back later for a citation.


Below are individual Rice 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.

Rice 2022-12 PSM FDR = 0.001Latest Build
  • Biosequence Set in FASTA format [737MB]
  • Database tables exported as mysql dump file [215MB]
  • Peptide CDS and chromosomal coordinates [482MB]
  • Peptide CDS coordinates [339MB]
  • Peptide sequences in FASTA format [6MB]


Complete description of each of the available download formats

Other Resources


We gratefully acknowledge the support for the Rice PeptideAtlas from the National Science Foundation grant DBI-1933311 “PTMexchange: Globally harmonized re-analysis and sharing of data on post-translational modifications” .