title: FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data.
abstract: A thorough understanding of the fragmentation processes in MS/MS can be a powerful tool in assessing the resulting peptide and protein identifications. We here present the freely available, open-source FragmentationAnalyzer tool (http://fragmentation-analyzer.googlecode.com) that makes it straightforward to analyze large MS/MS data sets for specific types of identified peptides, using a common set of peptide properties. This enables the detection of fragmentation pattern nuances related to specific instruments or due to the presence of post-translational modifications.
authors.affiliation: Department of Informatics, University of Bergen, Bergen, Norway. Harald.Barsnes@ii.uib.no
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
authors.forename: Ingvar
authors.initials: I
authors.lastname: Eidhammer
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D000595:Amino Acid Sequence; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D012984:Software; D013223:Statistics as Topic / Q000379:methods*
chemical_list: D010455:Peptides