Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France.

Over the last five years, the Human Proteome Organisation Proteomics Standards Initiative (HUPO PSI) has produced and released community-accepted XML interchange formats in the fields of mass spectrometry, molecular interactions and gel electrophoresis, have led the field in the discussion of the minimum information with which such data should be annotated and are now in the process of publishing much of this information. At this 4(th) Spring workshop, the emphasis was on consolidating this effort, refining and improving the existing models and in pushing these forward to align with more broadly encompassing efforts such as FuGE (Jones, A.R., Pizarro, A., Spellman, P., Miller, M., FuGE Working Group FuGE: Functional Genomics Experiment Object Model. OMICS 2006, 10, 179-184) and the Ontology for Biomedical Investigation (OBI). The effort to merge the existing mass spectrometry XML interchange formats, mzData and mzXML, into one single standard mzML yielded significant progress. Also the preliminary design of AnalysisXML was extended to include several new use cases and better support for quantification information. Finally the Molecular Interaction group discussed the development of a molecular interaction scoring system with accompanying gold standard data test sets.