title: Modification Site Localization in Peptides.
abstract: There are a large number of search engines designed to take mass spectrometry fragmentation spectra and match them to peptides from proteins in a database. These peptides could be unmodified, but they could also bear modifications that were added biologically or during sample preparation. As a measure of reliability for the peptide identification, software normally calculates how likely a given quality of match could have been achieved at random, most commonly through the use of target-decoy database searching (Elias and Gygi, Nat Methods 4(3): 207-214, 2007). Matching the correct peptide but with the wrong modification localization is not a random match, so results with this error will normally still be assessed as reliable identifications by the search engine. Hence, an extra step is required to determine site localization reliability, and the software approaches to measure this are the subject of this part of the chapter.
authors.affiliation: Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, USA. chalkley@cgl.ucsf.edu.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Chalkley
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D057166:High-Throughput Screening Assays; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000032:analysis*; D011499:Protein Processing, Post-Translational; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D057386:Search Engine; D012984:Software
chemical_list: D010455:Peptides; D020543:Proteome
keywords: False localization rate; Modification site localization; Peak picking