The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation at the 6th annual HUPO world congress updated the delegates on the current status of the ongoing work of this group. The new MS interchange format, mzML, had been entered into the HUPO document process immediately prior to the meeting and was already under active discussion by prospective users. It is anticipated this will become the de facto standard in this area in 2008. Minimal requirements documents are in the process of being published and proteomics journals are beginning to request data deposition as part of the manuscript submission process. The session ended with a lively debate on the practical implications these advances will have on daily laboratory work, on submission procedures and the tools which are being developed to assist in these activities.