Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search

J Proteome Res. 2015 Nov 6;14(11):4714-20. doi: 10.1021/acs.jproteome.5b00599. Epub 2015 Sep 29.

Abstract

Bottom-up proteomics database search algorithms used for peptide identification cannot comprehensively identify post-translational modifications (PTMs) in a single-pass because of high false discovery rates (FDRs). A new approach to database searching enables global PTM (G-PTM) identification by exclusively looking for curated PTMs, thereby avoiding the FDR penalty experienced during conventional variable modification searches. We identified over 2200 unique, high-confidence modified peptides comprising 26 different PTM types in a single-pass database search.

Keywords: G-PTM; Jurkat; Morpheus; PTM; acetylation; database search; phosphorylation; post-translational modification; proteomics.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Acetylation
  • Algorithms*
  • Animals
  • Data Mining / statistics & numerical data
  • Databases, Protein
  • Humans
  • Hydroxylation
  • Islets of Langerhans / chemistry
  • Islets of Langerhans / metabolism
  • Jurkat Cells
  • Male
  • Methylation
  • Mice
  • Mice, Inbred C57BL
  • Molecular Sequence Annotation
  • Peptide Fragments / chemistry*
  • Peptide Fragments / isolation & purification
  • Peptide Fragments / metabolism
  • Peptide Mapping
  • Phosphorylation
  • Protein Processing, Post-Translational*
  • Proteins / chemistry*
  • Proteins / isolation & purification
  • Proteins / metabolism
  • Proteomics / methods*
  • Software*

Substances

  • Peptide Fragments
  • Proteins