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ProteomicsA meta-analysis of phosphoproteomics datasets from Toxoplasma gondii
We performed a meta-analysis over 10 publicly available phosphoproteomics datasets available for Toxoplasma gondii, as part of the PTMeXchange project using standardised analysis pipelines. For the reference genome ME49, in total, 24360 phosphosites were identified at a minimum of 5% FLR in any data...
ORGANISM(S): Toxoplasma gondii 
2026-06-09 | PXD078724 | Pride
Phosphoproteomics Ptmexchange Reanalysis Public data Flr 
ProteomicsAn AI-ready phosphorylation meta-analysis for Saccharomyces cerevisiae.
We, the PTMeXchange Consortium, present a meta-analysis of eight high-quality data sets to map 56,694 phosphosites in brewer's yeast (Saccharomyces cerevisiae) using strict control for false identifications. Each site has been classified into the Gold-Silver-Bronze (GSB) categories depending on the ...
ORGANISM(S): Saccharomyces cerevisiae 
2025-12-16 | PXD071918 | Pride
ProteomicsA landscape analysis of human SUMOylation: A comprehensive meta-analysis of publicly available datasets
SUMOylation is an important but understudied post-translational modification (PTM) linked to diverse physiological and pathological processes. Various laboratories have developed protocols for identifying SUMOylation target sites using SUMO enrichment followed by mass spectrometry. As part of the PT...
ORGANISM(S): Homo sapiens 
2025-12-16 | PXD068489 | Pride
ProteomicsAcetylation in the human proteome: A meta-analysis of publicly available data sets
Datasets from the PRIDE repository were selected for re-analysis based on the following criteria: (i) human-derived samples enriched for acetylation; (ii) data generated using Thermo Fisher Scientific instruments; and (iii) availability of metadata, either through the original publication or by dire...
ORGANISM(S): Homo sapiens (Human) 
2026-06-09 | PXD079218 | Pride
Human Ptmexchange Flr Reanalysis Acetylation 
ProteomicsUbiquitination in the human proteome: A meta-analysis of publicly available data sets
Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme activation. Mass spectrometry-based proteomics has allowed proteome-scale quantification of hundred...
ORGANISM(S): Homo sapiens (Human) 
2026-06-09 | PXD068989 | Pride
Human Ubiquitination Ptmexchange Flr Reanalysis 
ProteomicsPhosphorylation in the Plasmodium falciparum proteome: A meta-analysis of publicly available data sets
Malaria is a deadly disease caused by Apicomplexan parasites of the Plasmodium genus. Several species of the Plasmodium genus are known to be infectious to human, of which P. falciparum is the deadliest. Post-translational modifications (PTMs) of proteins coordinate cell signalling and hence, regula...
ORGANISM(S): Plasmodium falciparum 
2023-11-22 | PXD046874 | Pride
Phosphoproteomics Ptmexchange Flr Public data Reanalysis 
ProteomicsA meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome
Abstract We have re-analysed publicly available mass spectrometry (MS) data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we have identified, 15522 phosphosites on Serine, Threonine and Tyrosine residues on rice proteins. The data has been loaded into UniProtKB, enabling...
ORGANISM(S): Oryza sativa (Rice) 
2023-11-08 | PXD046188 | Pride
Phosphoproteomics Ptmexchange Flr Public data Reanalysis 
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