Publishing large proteome datasets: scientific policy meets emerging technologies

Currently, there are various approaches to proteomic analyses based on either 2D gel or HPLC separation platforms, generating data of different formats, structures and types. Identification of these separated proteins or peptide fragments is typically achieved by mass spectrometry (MS) measurements that use either accurate mass measurements or fragmentation (MS-MS) information. Integrating the information generated from these different platforms is essential if proteomics is to succeed. A further challenge lies in generating standards that can accept the hundreds-of-thousands of mass spectra produced per analysis based on threshold or probability measurements. Finally, peer review and electronic publication processes will be crucial to the dissemination and use of proteomic information. Merging the policy requirements of data-intensive research with information technology will enable scientists to gain real value from global proteomics information.