Research

Proteome informatics

• http://www.proteosuite.org - Open-source software for the analysis of quantitative proteomics data.
• ProteoAnnotator - tools for proteogenomics, in collaboration with EuPathDB
• Multiple search engine framework. Web implementation, contact us for source code or executables (algorithm article, implementation article)
• Tools for exploiting ion mobility mass spectrometry - (article)
• The PSI semantic validator (article)
• Benchmarking label free quantitation

Pathogen bioinformatics

• Proteomics of Toxoplasma gondii (article)
• Proteogenomic annotation of Apicomplexa (see ProteoAnnotator website)
• Host-parasite interactions, modulation of the Host Cell Proteome (article)

Data standards and reporting guidelines

• The mzIdentML standard for peptide and protein identifications (article) and Java API jMzIdentML (article)
• Minimum information guidelines for Proteomics (article)
• The FuGE project (The Functional Genomics Experiment model, article)

Web databases

• The Allele Frequencies in Worldwide Populations database, developed by Faviel Gonzalez and led by Prof Derek Middleton, (article)
• Library of Apicomplexan Metabolic Pathways: LAMP developed by Achchuthan Shanmugasundram (article)

Code repositories

• Tools for ion mobility MS
• Java API for mzIdentML
• Java API for mzQuantML (beta)
• Java library of re-usable routines for processing mzIdentML files
• Java parsers for converting various data formats into mzIdentML
• Viewer for mzIdentML
• Main mzQuantML repository
• Validation software for mzQuantML
• Post-processing software for Progenesis LC-MS
• Proteosuite software integrated interface for quantitative proteomics
• Home page of mzIdentML resources - article
• Web interface to the multiple search engine approach - algorithm article, implementation article