PROTEOMICS PROJECTS
HUPO Publications Committee and PSI discuss standards This year’s spring meeting of the HUPO Proteomics Standards Initiative (PSI), held April 21–23, opened with a joint gathering of PSI and the HUPO Publications Committee. For the first time, the groups joined forces to invite academic and industrial researchers, software and instrument vendors, and journal representatives to share their views about proteomics guidelines and standards at a HUPO venue. Specifically, the topics included guidelines for the submission of proteomics manuscripts to journals and for documents related to data models and the minimum information about a proteomics experiment (MIAPE). No major decrees were handed down, but by the end of the meeting, attendees had a better understanding of the perspectives of the various stakeholders, says Chris Taylor, who is at the European Bioinformatics Institute (U.K.) and is a PSI member. According to Taylor, as planning began for this year’s spring meeting, PSI members realized that the two groups had a common interest: standard reporting methods for describing proteomics experiments. PSI currently is developing standard data formats that are instrument-independent for easy data exchange. The group is also producing a suite of MIAPE documents that specify key information for researchers to report when describing their experiments. Peipei Ping, who is at the David Geffen School of Medicine at the University of California, Los An-
geles, and is chair of the Publications Committee, says that the committee was originally convened to formulate publication guidelines for proteomics submissions to journals. The founding members were instrumental in creating the “MCP guidelines”, now known in the field as the “Paris guidelines”, which list the required and recommended elements of a proteomics research paper. Publication guidelines and standards initially were discussed among a small subset of stakeholders at a closed-door pre-meeting; later, all interested meeting attendees were invited to participate in an open panel discussion. “The Publications Committee wanted to facilitate communications” among all parties affected by these standards, says Ping. Although journal publication guidelines and PSI data standards seem very similar on the surface, there exist subtle differences that were discussed at the meeting. Researchers must record experimental details for either type of standard, but PSI standards require a researcher to only describe what happened in an experiment, whereas journal guidelines add a further requirement that researchers demonstrate a certain level of quality, explains Taylor. At this stage, no stakeholders were prepared to go so far as to recommend MIAPE compliance as a prerequisite to publication, but Taylor sees a role for PSI in making sure that its standards are at least in agreement with the journal guidelines so that parts of MIAPE
could be incorporated into those guidelines in the future. Attendees were also concerned about who would manage reporting standards and guidelines over the long term. As for data models and MIAPE documents, Taylor says that PSI is the obvious body. But the management of publishing guidelines is a more nebulous proposition. “With the journal guidelines, it appears that the mechanism is more ad hoc, where a group of willing people with appropriate expertise will come together, but it’s not clear what the long-term mechanism is here,” he explains. According to Taylor, journal representatives at the meeting said that they see themselves more as a pipeline for information than as a managing body for publishing guidelines. Journal reviewers, the representatives explained, have the ultimate say as to how guidelines are applied and which papers are published. “Given that PSI [exists] and that HUPO is now increasingly well thought of as a sponsoring organization, I think [PSI] is properly constituted to manage these sorts of things,” says Taylor. Guidelines and standards have been on the minds of researchers, bioinformaticians, instrument vendors, and journal representatives for a few years now, and the issue is not likely to go away anytime soon. As Ping says, “I think all parties recognized that this [topic] is something that we need to visit on a regular basis to incorporate new technologies and approaches.” —Katie Cottingham
GOVERNMENT AND SOCIETY
PSI announces deadlines for merging data formats On June 1, 2006, HUPO announced a series of timelines for the merger of mzData and mzXML into one unified data format to store spectral data and descriptions of mass spectrometer parameters. Called dataXML, the new MS data format will also feature tools for developers and users. The two formats were created a few years ago by members of groups with overlapping rosters. mzData was developed by members of the HUPO Proteomics Standards Initiative (PSI) and
mzXML by a group led by researchers at the Institute for Systems Biology, some of whom were also PSI members. Researchers involved with both projects realized last year that the formats could be merged into one unified model. PSI members plan to complete most of the tasks necessary for the merger by the end of 2006. The data model and an ontology model are scheduled to be completed by August. Additional features, such as documentation, a draft specification of schema, and an application programming interface (known as an API) should be finalized by Sep-
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tember. Two new programs, to be completed by December, will be included in dataXML: one to normalize files for random access and digital signatures, and another to make sure that the terms used in the model match the minimum information about a proteomics experiment (known as MIAPE) guidelines. To enable researchers to use the new format on a variety of MS instruments, PSI members will work with MS instrument and software vendors to create reference implementations of data converters. These converters also will be available in December.
