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Molecular & Cellular Proteomics Will Require Raw Data for Studies to be Published

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This story originally ran on Sept. 29.

TORONTO – The journal Molecular & Cellular Proteomics announced at the Human Proteome Organization annual conference that it will require researchers to submit their raw data to a public repository after their manuscripts have been accepted for publication.

The new policy will take effect after Jan. 1, 2010, and is part of new data submission guidelines the journal is implementing in the face of an evolving field that has made it increasingly difficult to assess the quality of research being done in proteomics, said Ralph Bradshaw, co-editor of MCP.

Overall, the goal of the guidelines, he said, is to provide enough information to explain an experiment and provide data to support the experimental results, so that other researchers will then be able to judge the reliability of the results.

"This is the future of proteomics," he said during a session on publishing in the field. "Unless we do this … we will continue to struggle with errors."

Under the new guidelines, all mass spectra "contributing to the described work" will need to be deposited in a repository such as Tranche, though that will not need to be done until the manuscript has been accepted.

MCP began recommending in 2005 that authors submit their more detailed data along with their manuscripts, then began making such data submissions a requirement a year later. That led other journals to take similar action, and funding agencies now also have data-submission guidelines in order for studies to get federal funding.

But Bradshaw said today that in the four years since MCP began its more stringent data-submission policy, the field has gotten increasingly challenging, making a proper evaluation of the quality of the studies impossible.

Each year, MCP receives about 600 manuscripts. Of that, 40 percent to 50 percent are returned because of missing mandatory data. Five percent to 10 percent fail a second time because they continue not to meet data submission guidelines, or they are not resubmitted. The overall acceptance rate of manuscripts is just under 30 percent, Bradshaw said, adding that number is expected to stay steady.

"Given these statistics, and the HUPO protein standards exercise" – in which only seven of 24 laboratories successfully identified all 20 proteins in a protein mixture sample [See PM 05/21/09] – "proteomics still has a major quality control problem in protein identification by mass spectrometry," Bradshaw said, adding that the situation for post-translation modifications is even worse.

Along with the new guideline for raw data, MCP is "tightening" its existing guidelines, such as requirements that researchers disclose the peak-list method or program, search engine, and sequence database used, as well as a study's false discovery rate.

Authors will also be required to submit all peptide sequences assigned to an identified protein, "noting any deviation from the expected protein cleavage specificity," Bradshaw said.

Quantitative data is also going to be required, as will PTM identification.

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