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| 52 | ProteomeXchange datasets |
| 266 | experiments |
| 39,480,811 | PSMs |
| 535,340 | distinct peptides |
| 17,858 | canonical Araport11 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.
Please note that this is a previous version of this PeptideAtlas. Browse the most recent Arabidopsis PeptideAtlas .
| Chromosome | Entries | Canonical | Uncertain | Redundant | Not 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% |
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” .