As more researchers adopt mass spectrometry for proteomics, experts have called for quality standards ensuring correct protein and peptide identifications in the growing proteomic literature. Last month, a panel of experts from academia and industry, as well as representatives of journals with an interest in proteomics, put forward draft guidelines, resulting from a workshop in Paris in May, that they hope will become widely accepted by journals as early as 2006.
According to proteomics researchers, the current proteomic literature is riddled with incorrect protein identifications. "There are probably papers where as much as 50 percent of the identifications were wrong," although these are extreme cases, said Ralph Bradshaw, editor-in-chief of Molecular and Cellular Proteomics and a professor of physiology and biophysics at the University of California, Irvine, medical school. "As a technology quickly takes over a field, and everybody jumps on the bandwagon, [with it comes] inexperience, and lack of understanding of pitfalls in the use of the technology leads to mistakes," he said.
"We all want to see the data that is published in journals to be as correct as possible," he said. The guidelines "only intended to do that, and nothing else."
"There are probably papers where as much as 50 percent of the identifications were wrong."
The new draft guidelines, posted on the Molecular and Cellular Proteomics website and other sites, are an amended and expanded version of the so-called Carr guidelines that were published by Steven Carr of the Broad Institute and five co-authors in MCP in April of last year and were adopted by MCP at that time (see PM 1/14/2005.)
During a comment period that ends Oct. 15, proteomics researchers are invited to send in their criticism and suggestions, which will be considered by a committee consisting of participants of the Paris meeting.
A final version is expected to be finished by the end of the year. The final guidelines will then be sent to all journals with an interest in proteomics papers, starting early next year, with the hope that they will adopt them, according to Bradshaw.
The 30 participants of the Paris workshop (60 were initially invited), supported by the American Society of Biochemistry and Molecular Biology, MCP's publisher, covered a much broader swath of the proteomics community than the authors of the Carr guidelines. Besides academic researchers, they included representatives from mass spec vendors Thermo Electron, Waters, and Applied Biosystems; bioinformatics firms Matrix Science and Beavis Informatics; drug makers Novartis, Amgen, Cellzome, and Biocrates Life Sciences; as well as representatives from the journals MCP, Analytical Chemistry, Journal of Proteome Research, Proteomics, and the Nature Publishing Group.
The revised rules, to be known as the "Paris guidelines", differ in a number of ways from the original Carr guidelines. Most significantly, the authors added a section on quantifiable mass spec data. They also rewrote a section referring to dealing with homologous proteins. Other than that, most of the changes were subtle, according to Bradshaw: "Nothing was really eliminated from the Carr guidelines, but they were certainly improved and tightened up."
Viewpoints varied most on the last point, which deals with whether or not researchers should provide access to their raw mass spec data â€" which requires large amounts of storage â€" and who will host these data. The current draft guidelines merely state that "authors are encouraged to provide access to raw MS data using other means, including group websites and public repositories, as they emerge, in addition to the journal itself." MCP, Bradshaw said, will set up a test repository for such data for articles it publishes at the Broad Institute this month, which will provide the server space.
Naturally for a field that still undergoes rapid technological development, even the final guidelines will be subject to change in the future, according to Bradshaw.
The main question for the guidelines' success is whether other journals â€" besides MCP â€" will adopt them in the end and make them mandatory for their authors.
"Our response will really depend on how these guidelines are accepted by the proteomics community," Kathy Aschheim, a senior editor of Nature Biotechnology who represented the Nature Publishing Group at the workshop, told ProteoMonitor. "If they are broadly accepted by this community, it's certainly likely that we will adopt them" for all of the group's journals that publish proteomics papers. However, it is not clear yet how NPG will judge the broad acceptance of the rules.
"We are very supportive of what the Paris group did," Bill Hancock, editor in chief of the Journal of Proteome Research, which is published by the American Chemical Society, told ProteoMonitor. After taking some time to get "some consensus" from the community, "[we will] post some version of it on our website," trying to make [the format] more user-friendly. Hancock, a professor of analytical and protein chemistry at Northeastern University, pointed out that archiving the raw mass spec files might be a problem, since there is no funding agency that might take on the task.
â€" Julia Karow ([email protected])