PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

TLDR

PhosphoSitePlus is a mammalian PTM knowledgebase containing over 330,000 non‑redundant sites, 95 % of which come from mass spectrometry, and includes a curated “Regulatory sites” dataset describing modification sites that control cellular processes. The database improves data reliability by reanalyzing over one million spectra with a common standard and filtering out sites with P > 0.05, and by integrating missense mutations from UniPROTKB, TCGA and other sources into the PTMVar dataset. The updated PSP releases two new downloads, including a PTMVar dataset that identifies over 25,000 PTM‑impacting missense variants—comprising 18,548 phosphorylation, 3,412 ubiquitylation, 2,316 acetylation, 685 methylation, and 245 succinylation sites—that can rewire signaling pathways.

Abstract

PhosphoSitePlus® (PSP, http://www.phosphosite.org/), a knowledgebase dedicated to mammalian post-translational modifications (PTMs), contains over 330 000 non-redundant PTMs, including phospho, acetyl, ubiquityl and methyl groups. Over 95% of the sites are from mass spectrometry (MS) experiments. In order to improve data reliability, early MS data have been reanalyzed, applying a common standard of analysis across over 1 000 000 spectra. Site assignments with P > 0.05 were filtered out. Two new downloads are available from PSP. The 'Regulatory sites' dataset includes curated information about modification sites that regulate downstream cellular processes, molecular functions and protein-protein interactions. The 'PTMVar' dataset, an intersect of missense mutations and PTMs from PSP, identifies over 25 000 PTMVars (PTMs Impacted by Variants) that can rewire signaling pathways. The PTMVar data include missense mutations from UniPROTKB, TCGA and other sources that cause over 2000 diseases or syndromes (MIM) and polymorphisms, or are associated with hundreds of cancers. PTMVars include 18 548 phosphorlyation sites, 3412 ubiquitylation sites, 2316 acetylation sites, 685 methylation sites and 245 succinylation sites.