Category Archives: 2010

FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data

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 … Continue reading

Posted in 2010, Publications

XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results

Identification of proteins by MS plays an important role in proteomics. A crucial step concerns the identification of peptides from MS/MS spectra. The X!Tandem Project (http://www.thegpm.org/tandem) supplies an open-source search engine for this purpose. In this study, we present an … Continue reading

Posted in 2010, Publications

OLS dialog: an open-source front end to the ontology lookup service

With the growing amount of biomedical data available in public databases it has become increasingly important to annotate data in a consistent way in order to allow easy access to this rich source of information. Annotating the data using controlled … Continue reading

Posted in 2010, Publications

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics

MS-based proteomics produces large amounts of mass spectra that require processing, identification and possibly quantification before interpretation can be undertaken. High-throughput studies require automation of these various steps, and management of the data in association with the results obtained. We … Continue reading

Posted in 2010, Publications