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HUPO’s PSI Preparing Papers on Three New MIAPE Modules for Publication in Early 2008

Fresh off the publication of a broad paper outlining its goals and processes, the Human Proteome Organization’s Proteomic Standards Initiative working group is putting the final touches on its first set of so-called “guidance” modules setting reporting standards for specific types of proteomics experiments.
Editors of modules — which cover mass spectrometry, mass spectrometry informatics, and gel electrophoresis — are currently addressing comments by outside commentators and incorporating them into the manuscripts, Chris Taylor, PSI cross-workgroup chair, told ProteoMonitor this week. Taylor is also a software engineer at the European Bioinformatics institute and the UK’s Natural Environment Research Council’s Environmental Bioinformatics Center.
In August, PSI published a parent paper outlining its initiative called “The minimum information about a proteomics experiment (MIAPE)” — an outline of PSI’s work in trying to set guidelines and reporting standards for the type of information researchers should deposit in a repository containing proteomics information. At the time, the group also published its first implementation module in another paper, “The minimum information required for reporting a molecular interaction experiment (MIMix)” [See PM 08/16/07].
The three modules currently in development, however, would represent PSI’s first papers specifically targeted to proteomics experiments. According to Taylor, they are expected to be ready for publication in Nature Biotechnology in early 2008.
“We’re just tying up loose ends with referee comments,” Taylor said. Because so many people have provided input into the three documents, the task is to decide which ones are the most meaningful and incorporate them into the modules.
“We’re more or less in the last round of that now,” he said.
HUPO’s initiative to create reporting standards for proteomics experiments has been a years-long effort — at HUPO’s annual conference next week in Seoul, one panel will mark PSI’s five-year anniversary and provide an update on its work. While there is widespread consensus that such standards are long overdue, there has been equal reluctance by many in the research community toward the effort [See PM 09/28/06].
But as funding agencies such as the National Institutes of Health and an increasing number of scientific journals put their support behind reporting standards, the proteomics community sees the writing on the wall.
“Given these background changes that are sort of permeating through the community … I think, in general people are accepting that they’re going to be told to do it fairly soon,” Taylor said.
The nature of the complaints against reporting standards has evolved as that realization has seeped through. Initially, some objected to reporting standards because they believed they would create additional work for researchers without providing any benefits, Taylor said. But, he noted, PSI has addressed those concerns by explaining how the adoption of such standards will improve the quality of the work.
On the other hand, there are still concerns in the community regarding the lack of tools that would allow researchers to follow the guidelines. “No one’s really going to be made to do this stuff until it’s fairly straightforward to do, until there are tools, there are databases and other resources,” Taylor said.
PSI has received verbal pledges from various vendors to create the tools necessary to make reporting the data more streamlined so that researchers will be able to easily produce reports that meet reporting-standards requirements, he said.

“Once you get away from the real core methods … you’re into this gray area where it’s more about who you can get to help than it is about which are the important ones.”

At the moment, PSI anticipates publishing a total of seven modules, not including the parent paper, though that number could change. Those modules cover column chromatography, capillary electrophoresis, gel informatics, gel electrophoresis, mass specs, mass spec informatics, and MIMix.
PSI is also considering a module on protein and peptide arrays though at this point the group has only talked about it, Taylor said.
PSI chose mass spec, mass spec informatics, and gel electrophoresis for its first proteomics-specific modules partly because each represents a major technology being used by proteomics researchers, and partly as a result of logistics, Taylor said.
It made sense to have modules on mass spectrometry get published earlier than the others because “that was the most growing need,” Taylor said. “This is where, for instance, Molecular & Cellular Proteomics saw the real damage was being done in proteomics papers: People’s use of statistics, people’s use of tools. And similarly, from several years back now, [it was] clear that mass specs were where we needed to focus on first.”
After the initial three modules, the column chromatography module is expected to be published first, followed by the gel informatics paper, and finally the capillary electrophoresis module, Taylor said.
However, he said, the order of publication of the modules will depend largely on how quickly PSI can find volunteers to review the modules for other technologies.
“Once you get away from the real core methods … you’re into this gray area where it’s more about who you can get to help than it is about which are the important ones,” Taylor said.
For the module on capillary electrophoresis, for example, PSI asked about a dozen researchers to review it. In the end, only two did so.
“It’s really just a pragmatic thing — where we can find an enthusiastic group of people to contribute, things will move more quickly. If it’s ‘blood out of stone’ time, then things will move more slowly.”

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