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 2022‑11	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 2022‑11	Visible on Mus musculus (Mouse) proteome		Results	Fasta file
Saccharomyces cerevisiae	Yeast	Phospho	N/A	Yeast Phospho 2024‑08	Visible on Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) proteome		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 2022‑04	In progress
Homo sapiens	Human	SUMO	N/A	Human SUMO 2025‑02	Visible on Homo sapiens (Human) proteome		Results	Fasta file
Homo sapiens	Human	Ubiquitination	N/A	Human Ubiquitination 2025-??	Visible on Homo sapiens (Human) proteome		Results	Fasta file
Homo sapiens	Human	Acetylation	N/A	Human SUMO 2025-??	Visible on Homo sapiens (Human) proteome		Results	Fasta file

PTM Builds in Progress

• Phosphorylation in Toxoplasma gondii

Publications (including Methods)

• 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 Jun 2;22(6):1828-1842. 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 Jul 1;21(7):1603-1615. PMCID: PMC9251759.
• Kalyuzhnyy A, Eyers PA, Eyers CE, Bowler-Barnett E, Martin MJ, Sun Z, Deutsch EW, Jones AR. J, Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation, 2022, J Proteome Res. 2022 Jun 3;21(6):1510-1524. 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