The HUPO Pre-Congress Proteomics Standards Initiative Workshop HUPO 5 th Annual World Congress Long Beach, CA, USA 28 October–1 November 2006 Sandra Orchard 1 , Andrew R. Jones 2 , Christian Stephan 3 and Pierre-Alain Binz 4, 5 1 EMBL Outstation – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK 2 School of Computer Science, University of Manchester, UK 3 Medizinisches Proteom-Center, Ruhr-Universität Bochum, Germany 4 Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland 5 Geneva Bioinformatics (GeneBio) SA, Geneva, Switzerland The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation provided an opportunity to update delegates on the progress of the work of the Human Proteome Organisation’s Proteomics Standards Initiative (HUPO-PSI) to develop and implement stand- ards in the field of proteomics. Significant advances have been made since the previous congress, with several of the interchange standards and minimal requirements documents being sub- mitted for publication in the literature and being more widely adopted by both manufacturers and data repositories. An exciting development over the interim twelve months is the ongoing merger of the two existing mass spectrometry standards, the PSI mzData and Institute for Sys- tems Biology mzXML, into a single product. This should be achieved by early in 2007. Received: January 5, 2007 Revised: January 19, 2007 Accepted: January 22, 2007 Keywords: Data standardization / Human Proteome Organisation / Proteomics Standards Initiative 1006 Proteomics 2007, 7, 1006–1008 Introduction Attendees to the Human Proteome Organisation’s Proteom- ics Standards Initiative (HUPO-PSI) were welcomed by the chair, Pierre-Alain Binz (Swiss Institute of Bioinformatics) who summarised the aims of the group, namely to produce, in collaboration with the scientific community, data exchange formats and minimal reporting requirements for the key processes in a typical proteomics workflow. These deliverables enable results from proteomics experiments to be accurately reported, the data to be exchanged between collaborators, deposited in public domain repositories and be available for use by other workers in the field. He then briefly outlined the program for the morning’s session before handing over to the first speaker. Molecular Interactions Sandra Orchard (EMBL-EBI, UK) summarised the work of the Molecular Interaction (MI) workgroup of HUPO-PSI. The MI group was the first PSI group to publish an XML interchange standard in 2004 with accompanying controlled vocabularies [1]. The PSI-MI XML1.0 was widely adopted by molecular interaction databases, many of whom made data available in this format, but it soon became apparent that the simple representation of protein:protein interaction data made pos- sible by this format was too restrictive for many users. To this end, a more flexible version 2.0 was developed and quickly Correspondence: Sandra Orchard, EBI, EMBL-European Bioinfor- matics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs. CB10 1SD, UK E-mail: orchard@ebi.ac.uk Fax: 144-1223-494-468 Abbreviations: HUPO-PSI, Human Proteome Organisation’s Pro- teomics Standards Initiative; MI, molecular interaction; MIMIx, Minimum Information Required for reporting a Molecular Inter- action Experiment REPORT DOI 10.1002/pmic.200700014  2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com