title: Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search.
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.
authors.affiliation: Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Shortreed
authors.affiliation: Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.
authors.forename: Craig D
authors.initials: CD
authors.lastname: Wenger
authors.affiliation: Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.
authors.forename: Brian L
authors.initials: BL
authors.lastname: Frey
authors.affiliation: Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.
authors.forename: Gloria M
authors.initials: GM
authors.lastname: Sheynkman
authors.affiliation: Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.
authors.forename: Mark
authors.initials: M
authors.lastname: Scalf
authors.affiliation: Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.
authors.forename: Mark P
authors.initials: MP
authors.lastname: Keller
authors.affiliation: Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.
authors.forename: Alan D
authors.initials: AD
authors.lastname: Attie
authors.affiliation: Department of Chemistry and ‡Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.
authors.forename: Lloyd M
authors.initials: LM
authors.lastname: Smith
mesh_terms: D000107:Acetylation; D000465:Algorithms; D000818:Animals; D057225:Data Mining / Q000706:statistics & numerical data; D030562:Databases, Protein; D006801:Humans; D006900:Hydroxylation; D007515:Islets of Langerhans / Q000737:chemistry / Q000378:metabolism; D019169:Jurkat Cells; D008297:Male; D008745:Methylation; D051379:Mice; D008810:Mice, Inbred C57BL; D058977:Molecular Sequence Annotation; D010446:Peptide Fragments / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D010449:Peptide Mapping; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D010446:Peptide Fragments; D011506:Proteins
keywords: G-PTM; Jurkat; Morpheus; PTM; acetylation; database search; phosphorylation; post-translational modification; proteomics