jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

FDRAnalysis: A Tool for the Integrated Analysis of Tandem Mass Spectrometry Identification Results from Multiple Search Engines

(2011) David C. Wedge et al.   JOURNAL OF PROTEOME RESEARCH

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

(2010) Thilo Muth et al.   PROTEOMICS

PRIDE Converter: making proteomics data-sharing easy

(2009) Harald Barsnes et al.   NATURE BIOTECHNOLOGY

OMSSA Parser: An open-source library to parse and extract data from OMSSA MS/MS search results

(2009) Harald Barsnes et al.   PROTEOMICS

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS