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.
Barsnes H, Eidhammer I, Martens L. FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data. Proteomics. 2010 Mar;10(5):1087-1090.