Overview

The PTMeXchange project has been established to make Post-Translational Modification (PTM) data FAIR (Findable, Accessible, Interoperable and Re-usable). Briefly, public proteomics datasets from ProteomeXchange resources are selected and manually curated. Then, the datasets are reanalysed using open analysis pipelines. The results are resubmitted to PRIDE and/or made available via PeptideAtlas. Finally, PTM data are integrated into UniProtKB, linking back to the original mass spectrometry evidence in ProteomeXchange resources. All produced data are released to the community.

Datasets

Species	Name	Modification	PXD	PeptideAtlas	UniProtKB*	Publication	Summary Results	Search Database
Oryza sativa	Rice	Phospho	PXD046188	Rice Phospho 2022‑04	Visible on Oryza sativa subsp. japonica (Rice) proteome	Ramsbottom et al., 2024	Results	Fasta file
Plasmodium falciparum	Malaria parasite	Phospho	PXD046874	Plasmodium Phospho 2023‑10	Visible on Plasmodium falciparum (isolate 3D7) proteome	Camacho et al., 2024	Results	Fasta file
Mus musculus	Mouse	Phospho	N/A	Mouse Phospho 2024‑02	Visible on Mus musculus (Mouse) proteome		Results	Fasta file
Saccharomyces cerevisiae	Yeast	Phospho	PXD071918	Yeast Phospho 2024‑08	Visible on Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) proteome	Boswell et al., 2026	Results	Fasta file
Trypanosoma brucei	African Trypanosomiasis	Phospho	N/A	T. brucei Phospho 2024‑12	Visible on Trypanosoma brucei brucei (strain 927/4 GUTat10.1) proteome		Results	Fasta file
Zea mays	Maize	Phospho	N/A	Maize Phospho 2024‑12	Visible on Zea mays (Maize) proteome		Results	Fasta file
Homo sapiens	Human	Phospho	N/A	Human Phospho 2025‑12	In progress
Homo sapiens	Human	SUMO	PXD068489	Human SUMO 2025‑02	Visible on Homo sapiens (Human) proteome	Al-Momani et al., 2026	Results	Fasta file
Homo sapiens	Human	Ubiquitination	PXD068989	Human Ubiquitination 2025‑11	Visible on Homo sapiens (Human) proteome		Results	Fasta file
Homo sapiens	Human	Acetylation	PXD079218	Human Acetylation 2026‑04	Visible on Homo sapiens (Human) proteome		Results	Fasta file
Homo sapiens	Human	Methylation	PXD076372	Human Methylation 2026‑04	Visible on Homo sapiens (Human) proteome		Results	Fasta file
Toxoplasma gondii	Infectious agent of toxoplasmosis	Phospho	PXD078724	T. gondii Phospho 2025‑05	Visible on Toxoplasma gondii (strain ATCC 50611 / Me49) proteome		Results	Fasta file

*For access on UniProtKB, please follow this guide.

PTM Builds in Progress

• Phosphorylation in Arabidopsis thaliana

Publications (including Methods)

• Boswell EL, Ramsbottom KA, Fan J, Perez-Riverol Y, Bowler-Barnett EH, Sun Z, Mesdaghi S, Rigden DJ, Martin MJ, Deutsch EW, Vizcaíno JA, Jones AR, An AI-Ready Phosphorylation Meta-Analysis for Saccharomyces cerevisiae, 2026, J Proteome Res. 2026, doi: 10.1021/acs.jproteome.5c01263. PMCID: PMC13247961.
• Al-Momani SS, Ramsbottom K, Collins A, Boswell E, Hendriks IA, Nielsen ML, Vertegaal ACO, Hay RT, Sun Z, Riverol YP, Bowler-Barnett EH, Martin MJ, Fan J, Sadanandom A, Deutsch EW, Vizcaíno JA, Jones AR, A Landscape Analysis of Human SUMOylation, 2026, Mol Cell Proteomics. 2026, doi: 10.1016/j.mcpro.2026.101571. PMCID: PMC13213312.
• Martin Camacho O, Ramsbottom KA, Prakash A, Sun Z, Perez-Riverol Y, Bowler-Barnett E, Martin MJ, Fan J, Deutsch EW, Vizcaino JA, Jones AR, Phosphorylation in the Plasmodium falciparum Proteome: A Meta-Analysis of Publicly Available Data Sets, 2024, J Proteome Res. 2024, doi: 10.1021/acs.jproteome.4c00418. PMCID: PMC11629380.
• Ramsbottom KA, Prakash A, Perez-Riverol Y, Martin Camacho O, Sun Z, Bowler-Barnett E, Martin MJ, Fan J, Chebotarov D, McNally KL, Deutsch EW, Vizcaino JA, Jones AR, A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome, 2024, J Proteome Res. 2024, doi: 10.1021/acs.jproteome.4c00187. PMCID: PMC11232104.
• Camacho OM, Ramsbottom KA, Collins A, Jones AR, Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets, 2023, J Proteome Res. 2023, doi: 10.1021/acs.jproteome.2c00823. PMCID: PMC10243108.
• Ramsbottom KA, Prakash A, Riverol YP, Camacho OM, Martin MJ, Vizcaino JA, Deutsch EW, Jones AR, Method for Independent Estimation of the False Localization Rate for Phosphoproteomics, 2022, J Proteome Res. 2022, doi: 10.1021/acs.jproteome.1c00827. PMCID: PMC9251759.
• Kalyuzhnyy A, Eyers PA, Eyers CE, Bowler-Barnett E, Martin MJ, Sun Z, Deutsch EW, Jones AR, Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation, 2022, J Proteome Res. 2022, doi: 10.1021/acs.jproteome.2c00131. PMCID: PMC9171898.

Members

The current members of the Consortium are: PRIDE (EMBL-EBI, Cambridge, UK), PeptideAtlas (ISB, Seattle, WA, USA), UniProt (EMBL-EBI, Cambridge, UK), University of Liverpool (Liverpool, UK).

We welcome other members to join these efforts.

Funding

This project is funded by NSF and BBSRC.

National Science Foundation
Biotechnology and Biological Sciences Research Council