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Full 2022-06 Build Summary
115ProteomeXchange datasets
369experiments
70,470,125PSMs
596,839distinct peptides
18,267canonical core proteins

About

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

Publicly-available Arabidopsis thaliana columbia-0 datasets were downloaded from ProteomeXchange and reprocessed from the raw files using the Trans-Proteomic Pipeline suite of tools. A publication describing the build is available.

Explore

SEARCH(e.g. AT1G01090.1)

Chromosome Summary

ChromosomeEntriesCanonicalUncertainRedundantNot Observed
M 35 27 77.1% 5 14.3% 0 0.0% 3 8.6%
C 79 63 79.7% 12 15.2% 0 0.0% 4 5.1%
1 7,156 4,730 66.1% 502 7.0% 384 5.4% 1,540 21.5%
2 4,317 2,762 64.0% 290 6.7% 240 5.6% 1,025 23.7%
3 5,460 3,630 66.5% 353 6.5% 296 5.4% 1,181 21.6%
4 4,180 2,788 66.7% 282 6.7% 247 5.9% 863 20.6%
5 6,332 4,267 67.4% 412 6.5% 373 5.9% 1,280 20.2%
2022-06 Total 27,559 18,267 66.3% 1,856 6.7% 1,540 5.6% 5,896 21.4%

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

Download

Below are individual Arabidopsis thaliana 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.

A. thaliana 2022-06 PSM FDR = 0.0008Latest Build
  • Biosequence Set in FASTA format [132MB]
  • Peptide CDS and chromosomal coordinates [377MB]
  • Peptide CDS coordinates [223MB]
  • Peptide sequences in FASTA format [17MB]
  • Peptide sequences in GFF format [19MB]
A. thaliana 2021-03 PSM FDR = 0.001
  • Biosequence Set in FASTA format [170MB]
  • Database tables exported as TSV dump file [5GB]
  • Database tables exported as mysql dump file [4GB]
  • Peptide CDS and chromosomal coordinates [331MB]
  • Peptide CDS coordinates [195MB]
  • Peptide sequences in FASTA format [15MB]

Help

Complete description of each of the available download formats

Other Resources

Acknowledgements

We gratefully acknowledge the support for the Arabidopsis PeptideAtlas from NSF grant 1922871 “TRTech-PGR: A PeptideAtlas for Arabidopsis thaliana and other plant species; harnessing world-wide proteomics data and mining for biological features”.