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PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.

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Summary
This summary is machine-generated.

PhosphoSitePlus (PSP) enhances mammalian post-translational modification (PTM) data reliability by reanalyzing mass spectrometry data. New datasets highlight regulatory sites and PTMVars, linking genetic variants to diseases and signaling pathway rewiring.

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Area of Science:

  • Biochemistry
  • Genomics
  • Bioinformatics

Background:

  • Mammalian post-translational modifications (PTMs) are crucial for cellular processes.
  • PhosphoSitePlus (PSP) is a comprehensive database of PTMs, primarily derived from mass spectrometry (MS).
  • Ensuring data reliability in large PTM datasets is essential for biological research.

Purpose of the Study:

  • To improve the reliability of existing mass spectrometry data in the PhosphoSitePlus database.
  • To introduce new curated datasets for enhanced data utility.
  • To identify and characterize PTMs impacted by genetic variants (PTMVars) and their potential roles in disease.

Main Methods:

  • Reanalysis of over 1,000,000 mass spectrometry spectra using a common analysis standard.
  • Filtering of site assignments with P > 0.05 to enhance data quality.
  • Integration of missense mutation data from UniPROTKB, TCGA, and other sources with PTM data.

Main Results:

  • Over 330,000 non-redundant PTMs are available in PSP, with >95% from MS experiments.
  • Reanalysis improved data reliability by applying consistent standards and filtering low-confidence sites.
  • Two new datasets were released: 'Regulatory sites' and 'PTMVar', identifying over 25,000 PTMVars.
  • PTMVars link missense mutations to over 2000 diseases and hundreds of cancers, including specific counts for phosphorylation, ubiquitylation, acetylation, methylation, and succinylation sites.

Conclusions:

  • The reanalysis of MS data significantly enhances the reliability of the PhosphoSitePlus PTM database.
  • The new 'Regulatory sites' and 'PTMVar' datasets provide valuable resources for understanding PTM regulation and variant-associated diseases.
  • PTMVars represent a critical intersection of genetic variation and PTMs, offering insights into signaling pathway rewiring and disease mechanisms.