115	ProteomeXchange datasets
369	experiments
70,470,125	PSMs
596,839	distinct peptides
18,267	canonical 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)

BROWSE

Chromosome Summary

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%

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%

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

van Wijk et al, The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource, published in The Plant Cell (2021 Aug 19) -- [ Pubmed ]

Short ICAR 2021 presentation of the 2021 Arabidopsis PeptideAtlas by Klaas Van Wijk -- [8 minute video on YouTube]

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”.