6	datasets
29	experiments
590	MS runs
21,941,816	spectra searched
1,665,362	PSMs
61,552	distinct peptides
5,606	canonical proteins

About

The Human Methylation Proteome PeptideAtlas provides a compendium of results from uniformly reprocessed mass spectrometry proteomics datasets.

Available datasets of Human Methylation Proteome 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 Human Methylation Proteome PeptideAtlas build is in progress.

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

Download

Below are individual Human Methylation Proteome 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.

Human Methylation 2026-04 PSM FDR = 0.00001Latest Build

Biosequence Set in FASTA format [458MB]
Database tables exported as TSV dump file [68MB]
Database tables exported as mysql dump file [163MB]
Peptide CDS and chromosomal coordinates [200MB]
Peptide CDS coordinates [122MB]
Peptide sequences in FASTA format [1MB]

Help

Complete description of each of the available download formats

Other Resources

Acknowledgements

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