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Full 2021-03 Build Summary
52ProteomeXchange datasets
266experiments
39,480,811PSMs
535,340distinct peptides
17,858canonical Araport11 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 122 15 12.3% 10 8.2% 17 13.9% 80 65.6%
C 88 59 67.0% 15 17.0% 7 8.0% 7 8.0%
1 7,156 4,622 64.6% 545 7.6% 397 5.5% 1,592 22.2%
2 4,317 2,695 62.4% 291 6.7% 247 5.7% 1,084 25.1%
3 5,460 3,561 65.2% 365 6.7% 308 5.6% 1,226 22.5%
4 4,180 2,723 65.1% 306 7.3% 230 5.5% 921 22.0%
5 6,332 4,183 66.1% 410 6.5% 394 6.2% 1,345 21.2%
2021-03 Total 27,655 17,858 64.6% 1,942 7.0% 1,600 5.8% 6,255 22.6%
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 2021-03 PSM FDR = 0.001Latest Build
  • 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” .