115 | ProteomeXchange datasets |
369 | experiments |
70,470,125 | PSMs |
596,839 | distinct peptides |
18,267 | canonical core proteins |
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.
Chromosome | Entries | Canonical | Uncertain | Redundant | Not 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% |
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.
Complete description of each of the available download formats
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”.