Both the generation and the analysis of proteomics data are now widespread, and high-throughput approaches are commonplace. Protocols continue to increase in complexity as methods and technologies evolve and diversify. To encourage the standardized collection, integration, storage and dissemination of proteomics data, the Human Proteome Organization's Proteomics Standards Initiative develops guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry. This paper describes the processes and principles underpinning the development of these modules; discusses the ramifications for various interest groups such as experimentalists, funders, publishers and the private sector; addresses the issue of overlap with other reporting guidelines; and highlights the criticality of appropriate tools and resources in enabling 'MIAPE-compliant' reporting. ; Taylor, Chris F. Paton, Norman W. Lilley, Kathryn S. Binz, Pierre-Alain Julian, Randall K., Jr. Jones, Andrew R. Zhu, Weimin Apweiler, Rolf Aebersold, Ruedi Deutsch, Eric W. Dunn, Michael J. Heck, Albert J. R. Leitner, Alexander Macht, Marcus Mann, Matthias Martens, Lennart Neubert, Thomas A. Patterson, Scott D. Ping, Peipei Seymour, Sean L. Souda, Puneet Tsugita, Akira Vandekerckhove, Joel Vondriska, Thomas M. Whitelegge, Julian P. Wilkins, Marc R. Xenarios, Ioannnis Yates, John R., III Hermjakob, Henning 45 NATURE PUBLISHING GROUP NEW YORK 199WL