A meta-analysis of phosphoproteomics datasets from Toxoplasma gondii
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ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Toxoplasma Gondii
SUBMITTER: 
Shengbo Wang
LAB HEAD: Andy Jones
PROVIDER: PXD078724 | Pride | 2026-06-09
REPOSITORIES: Pride
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Project description: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 confidence of identification. Of the identified phosphorylation sites, 22,311 (39.4%) were classified as Gold, 9,890 (17.4%) were classified as Silver and 24,493 (43.2%) were classified as Bronze. Among the gold sites, 82% occurred on serine, 17% occurred on threonine and just 1% occurred on tyrosine.
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Project description:Phosphoproteomics methods are commonly employed in labs to identify and quantify the sites of phosphorylation on proteins. In recent years, various software tools have been developed, incorporating scores or statistics related to whether a given phosphosite has been correctly identified, or to estimate the global false localisation rate (FLR) within a given data set for all sites reported. These scores have generally been calibrated using synthetic data sets, and their statistical reliability on real datasets is largely unknown. As a result, there is considerable problem in the field of reporting incorrectly localised phosphosites, due to inadequate statistical control. In this work, we develop the concept of using scoring and ranking modifications on a decoy amino acid, i.e. one that cannot be modified, to allow for independent estimation of global FLR. We test a variety of different amino acids to act as the decoy, on both synthetic and real data sets, demonstrating that the amino acid selection can make a substantial difference to the estimated global FLR. We conclude that while several different amino acids might be appropriate, the most reliable FLR results were achieved using alanine and leucine as decoys, although we have a preference for alanine due to the risk of potential confusion between leucine and isoleucine amino acids. We propose that the phosphoproteomics field should adopt the use of a decoy amino acid, so that there is better control of false reporting in the literature, and in public databases that re-distribute the data.
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