M E E T I N G
N E W S
Katie Cottingham reports from the Sixth Siena Meeting: From Genome to Proteome—Siena, Italy.
1108
Bradshaw
COURTESY OF DUNN
Guidelines for reporting proteomics data were the subject of a roundtable discussion led by a group of editors from the journals Molecular & Cellular Proteomics (MCP) and Proteomics at this year’s Siena Meeting. In June 2004, MCP published new guidelines for submissions (Mol. Cell. Proteomics 2004, 3, 531–533), and the discussion was an opportunity for researchers and journal editors to air their opinions. Under the MCP guidelines, which could be adopted in some form by other journals in the future, researchers are expected to submit numerous details about how they identified peptides and proteins in their experiments. According to Ralph A. Bradshaw, editor of MCP, he and the associate editors at the journal became concerned two years ago that erroneous protein identifications were seeping into the literature. Bradshaw says that the guidelines should make an author’s identification method more transparent to readers by requiring the inclusion of additional information, such as the name and version of the search engine used, sequence coverage data, and justification for protein assignments that are based on a single peptide. “The reader needs to be provided with some estimate of reliability,” he explains. After several internal discussions, a committee led by Steve Carr, an associate editor of MCP, finally hammered out the guidelines. “We didn’t think [the guidelines] were necessarily perfect, but we thought they were a good first pass,” says Bradshaw. He describes the document as a “work in progress” that is intended to generate discussion. Ultimately, Bradshaw hopes the proteomics community will agree on a set of universal guidelines for submissions to journals. To accomplish this goal, he is in contact with William Hancock, editor-in-chief of JPR, Michael Dunn, editor-in-chief of Proteomics, and Chris Taylor, who is a member of HUPO’s Protein Standards Initiative (PSI). Dunn says that the PSI is also trying to develop proteomics standards,
COURTESY OF BRADSHAW
Journals consider standardizing proteomics papers
Dunn
Hancock
including defining what constitutes the minimum information about a proteomics experiment, or MIAPE. Bradshaw plans to hold a workshop on the topic next spring. Journal editors and board members agree that meeting the guidelines should not be a burden for researchers and that having a policy will help keep the quality of submissions high. Ron Beavis, a member of JPR’s editorial advisory board, says, “I think most of the people in the community are coming to
Journal of Proteome Research • Vol. 3, No. 6, 2004
the realization that supplying the sort of data that is suggested in the MCP document really doesn’t hurt.” And according to Hancock, the reward of publishing in a high-quality journal will provide enough motivation for researchers to play by the rules. In describing how the guidelines will be implemented at MCP, Bradshaw says, “I see them as somewhere between suggestions and hard rules.” Hancock says that such guidelines would be recommendations that authors should strive to follow because reviewers will have them in mind when they assess a paper for JPR. Both editors stress that reviewers should still have the freedom to be flexible and to use their own judgment. Scott Patterson, a senior editor of Proteomics, explains that guidelines could become mandatory over time but with the caveat that they be fair. All laboratories must have access to the resources that are necessary to meet the specifications, to ensure that no one is at a disadvantage, he adds. One controversial topic included in the MCP document is the suggestion that researchers submit all their MS/MS spectra to a repository. “The major advantage of that is people can really work on the data and see what’s going on,” says Denis Hochstrasser, who serves on the editorial boards of MCP and Proteomics and will join JPR’s board in 2005. But some experts are afraid that they may be scooped by their own data if they are available for mining by competitors. And even if the journals decide to implement a repository, editors say that the data files generated in proteomics experiments are just too large for the journals to handle. Dunn says, “I think [a repository] is a more long-term issue that has to be done by the whole community with other initiatives, not just the journals.” Although many researchers and editors say that the guidelines still need some work, they agree that MCP’s attempt is a good first step. But even when a “final” set of guidelines is published, experts say that journals must remain flexible to keep up with the fast pace of innovation in the proteomics field. Hochstrasser says that editors needn’t be too worried about setting guidelines, however. “Standards establish themselves,” he says. “When we get better, standards become obvious.”
HUPO setting standards for proteomics data As the various HUPO initiatives and other proteomics projects produce data, the Proteomics Standards Initiative (PSI) has been working to establish standards for analyzing and storing them. This effort is especially important as highthroughput proteomics approaches become more widespread and techniques increase in complexity, according to Rolf Apweiler at the European Bioinformatics Institute (EBI). A PSI committee is currently hashing out the so-called MIAPE, the minimum information about a proteomics experiment, which would have to be provided for every experiment. One of the committee’s first tasks is to establish a comprehensive list of the official terms that will be used and their definitions, known as the controlled vocabulary. A draft, which builds on the terminology established by IUPAC and the American Society for Mass Spectrometry, is posted on the PSI website, http://psidev. sourceforge.net, and the release of a usable version is scheduled for the end of 2004. A PSI object model to describe the various aspects of an experiment is also under development. For researchers working specifically on molecular interactions, the Molecular Interaction Format defines a minimal data model that allows scientists to provide core data with references and simplifies synchronization among different databases. All of the IMEx databases have agreed that as of January 1, 2005, a researcher can submit data to any single database, and within five business days the data will be deposited in all other IMEx databases. Data that were deposited previously will eventually be shared among all databases. On the MS front, PSI is nearly ready to launch mzData, a standard format for storing MS data. Three instrument companies, Protagen/Bruker, Shimadzu/ Kratos, and Agilent, say that they are in various stages of implementing it for their mass spectrometers. Two new search engines, Aldente and Phenyx, both from SIB (Switzerland), will make use of mzData as an input format. Still under development is mzIdent, a stan-
dard format that could be used to store the results from search engines that identify proteins. One possible repository for proteomics data is the PRIDE database, an XML data repository and data transfer format for protein identifications by MS and supporting evidence. PRIDE is a public, open-source repository, but a research group can limit access to a few specific collaborators, according to Phil Jones of EBI. Because PRIDE was designed before the PSI began, it will require some additional work to be sure it’s compatible with mzData and mzIdent. However, it is intended to be complementary to those efforts, Jones says.
Rajendrani Mukhopadhyay reports from MicroTAS 2004— Malmö, Sweden. Microfluidic chip for 2DE
the proteins by SDS gel electrophoresis. The two sets of channels are staggered relative to each other to ensure the complete transfer of the proteins from the first dimension to the second dimension. DeVoe and colleagues also have a prototype of the chip that can interface with a MALDI target. In this prototype, a trypsin-coated polytetrafluoroethylene (PTFE) membrane is attached to the end of the second-dimension channels. The proteins are digested while passing through the porous PTFE membrane, and the resulting peptides are electrosprayed from the membrane surface onto the MALDI target. DeVoe says that the electrosprayed spots on the MALDI target are concentrated and uniform. “We have
