title: Global Post-Translational Modification Discovery.
abstract: A new global post-translational modification (PTM) discovery strategy, G-PTM-D, is described. A proteomics database containing UniProt-curated PTM information is supplemented with potential new modification types and sites discovered from a first-round search of mass spectrometry data with ultrawide precursor mass tolerance. A second-round search employing the supplemented database conducted with standard narrow mass tolerances yields deep coverage and a rich variety of peptide modifications with high confidence in complex unenriched samples. The G-PTM-D strategy represents a major advance to the previously reported G-PTM strategy and provides a powerful new capability to the proteomics research community.
authors.affiliation: Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States.
authors.forename: Qiyao
authors.initials: Q
authors.lastname: Li
authors.affiliation: Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Shortreed
authors.forename: Craig D
authors.initials: CD
authors.lastname: Wenger
authors.affiliation: Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States.
authors.forename: Brian L
authors.identifier: 0000-0002-0397-7269
authors.initials: BL
authors.lastname: Frey
authors.affiliation: Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States.
authors.forename: Leah V
authors.initials: LV
authors.lastname: Schaffer
authors.affiliation: Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States.
authors.forename: Mark
authors.initials: M
authors.lastname: Scalf
authors.affiliation: Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States.
authors.forename: Lloyd M
authors.initials: LM
authors.lastname: Smith
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence / Q000235:genetics*; D006801:Humans; D011499:Protein Processing, Post-Translational / Q000235:genetics*; D040901:Proteomics; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
keywords: G-PTM-D; database search; post-translational modification discovery; proteomics