title: Software eyes for protein post-translational modifications.
abstract: Post-translational modifications (PTMs) are critical to almost all aspects of complex processes of the cell. Identification of PTMs is one of the biggest challenges for proteomics, and there have been many computational studies for the analysis of PTMs from tandem mass spectrometry (MS/MS). Most early PTM identification studies have been performed by matching MS/MS data to protein databases, using database search tools, but they are prohibitively slow when a large number of PTMs is given as a search parameter. In this article, we present recent developments to search for more types of PTMs and to speed up the search, and discuss many computational issues and solutions in terms of identifying multiply modified peptides or searching for all possible modifications at once in unrestrictive mode. Apart from the most common type of PTMs involving covalent addition of functional groups to proteins, PTMs such as disulfide linkage require dedicated software for the analysis because they may involve cross-linking between two different parts of proteins. Finally, methods for identification of protein disulfide bonds are presented.
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, 92093; Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, 92093.
authors.forename: Seungjin
authors.initials: S
authors.lastname: Na
authors.forename: Eunok
authors.initials: E
authors.lastname: Paek
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D030562:Databases, Protein; D004220:Disulfides / Q000032:analysis* / Q000737:chemistry; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D010446:Peptide Fragments / Q000032:analysis*; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D040901:Proteomics / Q000295:instrumentation / Q000379:methods; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D004220:Disulfides; D010446:Peptide Fragments; D011506:Proteins
keywords: computational proteomics; post-translational modification; software; tandem mass spectrometry