Category Archives: 2010

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

Posted on March 17, 2011 by

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

Posted on March 17, 2011 by

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 … Continue reading →

Posted in 2010, Publications

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

Posted on March 17, 2011 by

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

Posted on March 17, 2011 by

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