19	datasets
64	experiments
992	MS runs
49,833,175	spectra searched
5,682,024	PSMs
360,826	distinct peptides
6,773	canonical proteins

About

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

Available datasets of Arabidopsis thaliana Phospho enriched samples were reprocessed from the raw files using the Trans-Proteomic Pipeline suite of tools.

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All detected canonical proteins

Chromosome Summary

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

A publication describing the Arabidopsis thaliana Phosphoproteome PeptideAtlas build is in progress.

For now, please just reference this URL, and check back later for a citation.

Download

Below are individual Arabidopsis thaliana Phosphoproteome 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.

Arabidopsis Phospho 2026-08 PSM FDR = 0.0003Latest Build

Biosequence Set in FASTA format [55MB]
Database tables exported as TSV dump file [50MB]
Database tables exported as mysql dump file [45MB]
Peptide CDS and chromosomal coordinates [19MB]
Peptide CDS coordinates [9MB]
Peptide sequences in FASTA format [2MB]

Help

Complete description of each of the available download formats

Other Resources

PTMeXchange

Acknowledgements

We gratefully acknowledge the support for the Mouse Phospho PeptideAtlas from the National Science Foundation grant DBI-1933311 “PTMexchange: Globally harmonized re-analysis and sharing of data on post-translational modifications” .