gpmdb

is a Data Source.

The Global Proteome Machine Database (GPMDB) stores peptide and protein identifications from tandem mass spectrometry experiments, reprocessed with the Global Proteome Machine pipeline and the X! Tandem search engine. It reports observed peptide and protein evidence, post-translational modifications and single amino acid variants across a very large number of public datasets, mapped mainly to Ensembl protein accessions. Since 2025-02-19 the GPMDB web interface rejects queries from US IP addresses; the REST API still answered from a US address on 2026-10-04.

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Domains

proteomics

License

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Homepage

gpmdb

Repository

Unknown

External IDs

Product Summary

Products

From this Resource
ID Name URL Category Format Description
gpmdb.portal ⚠ GPMDB Web Interface gpmdb.thegpm.org Graphical Interface http GPMDB web interface for searching pep...
gpmdb.api GPMDB REST API 1 Programming Interface json GPMDB REST API (version 2015.02.19) r...
gpmdb.xtandem X! Tandem tandem Process ❔ X! Tandem, the open source search eng...
From other Resources
ID Name URL Category Format Relation Description
omicsdi.portal OmicsDI Portal www.omicsdi.org Graphical Interface http had primary source Web portal for searching and browsing...
omicsdi.api OmicsDI API index.html Programming Interface http had primary source Swagger-documented web service for pr...

Details

Global Proteome Machine Database

GPMDB collects peptide and protein identifications from public tandem mass spectrometry data, reprocessed with the Global Proteome Machine (GPM) pipeline and the X! Tandem search engine. For each protein it reports how often it was observed, the peptides seen, the best expectation values, observed post-translational modifications and single amino acid variants. Proteins are keyed mainly by Ensembl protein accessions.

Access

  • Web interface: https://gpmdb.thegpm.org/. A GPM blog post of 2025-02-19 says that, because of the trade dispute between the USA and Canada, US IP addresses can no longer query GPMDB. The interface returned HTTP 403 from a US address on 2026-10-04.
  • REST API: https://rest.thegpm.org/1 lists its endpoints, such as /1/protein/count/acc=ACC and /1/peptide/count/seq=SEQ. It answered from a US address on 2026-10-04. The API reports version 2015.02.19. Its listing points to documentation on wiki.thegpm.org, which did not respond.
  • X! Tandem: the search engine is distributed from https://www.thegpm.org/tandem/ under the Artistic License.

License

The GPM site carries a copyright notice (The Global Proteome Machine, 2024) and states no data license. X! Tandem and its documentation are under the Artistic License.

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Created: October 04, 2026 | Last modified: October 04, 2026