Further Steps in Standardisation Report of the Second Annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17–20 th April 2005)

Abstract The spring workshop of the HUPO‐PSI convened in Siena to further progress the data standards which are already making an impact on data exchange and deposition in the field of proteomics. Separate work groups pushed forward existing XML standards for the exchange of Molecular Interaction data (PSI‐MI, MIF) and Mass Spectrometry data (PSI‐MS, mzData) whilst significant progress was made on PSI‐MS' mzIdent, which will allow the capture of data from analytical tools such as peak list search engines. A new focus for PSI (GPS, gel electrophoresis) was explored; as was the need for a common representation of protein modifications by all workers in the field of proteomics and beyond. All these efforts are contextualised by the work of the General Proteomics Standards workgroup; which in addition to the MIAPE reporting guidelines, is continually evolving an object model (PSI‐OM) from which will be derived the general standard XML format for exchanging data between researchers, and for submission to repositories or journals.