title: MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results.
abstract: MS-based protein identification is an important part of both gel-based and gel-free proteome studies. The MASCOT search engine (http://www.matrixscience.com) provides one of the most popular automated algorithms for this task. Here we present an open-source software library written in Java that parses raw MASCOT results into an easily accessible and fully functional object model (http://genesis.ugent.be/MascotDatfile). Several scripts based on this library are provided as examples, allowing direct automation of important routine tasks involved in processing peptide identifications.
authors.affiliation: Department of Biochemistry and Medical Protein Research, Faculty of Medicine and Health Sciences, Flanders Interuniversity Institute for Biotechnology, Ghent University, Ghent, Belgium.
authors.forename: Kenny
authors.initials: K
authors.lastname: Helsens
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.forename: Joël
authors.initials: J
authors.lastname: Vandekerckhove
authors.forename: Kris
authors.initials: K
authors.lastname: Gevaert
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D030562:Databases, Protein; D019151:Peptide Library; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D019151:Peptide Library