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J Biomol Tech. 2010 September; 21(3 Suppl): S14.
PMCID: PMC2918054

Publishing Standards for Proteomics and Next-Generation Sequencing Data

R. Chalkley
Department of Pharmaceutical Chemistry and the NCRR Mass Spectrometry Facility, University of California, San Francisco, CA, United States



As technology advances, the standards and rules for reporting data also change. In 2005, a set of guidelines for reporting proteomic data based on the mass spectrometric identification of peptides and proteins was established and subsequently adopted wholly or in part by several journals.While this set of requirements had the desired effect of focusing attention on the problems associated with most proteomic experiments, it was viewed by most people, as “a work in progress”. Importantly, the initial group, who were involved in the drafting of the “Paris” guidelines, accepted several compromises so as not to overburden authors in the reporting of their results. In the spring of the past year, it was deemed time to re-examine these guidelines, and the underlying bases for selecting them, and a group of some two dozen “stakeholders”, i.e. individuals with a range of expertise in this area, was convened with the view of updating them and to consider ways to make them more effective in advancing the field of proteomics. Among other changes, it was concluded that public data repositories for both processed and raw data had improved and could now serve some of the functions previously provided by journals. As this submitted information gives important support to maintain the integrity of the reported identifications and can also be further interrogated and analyzed to extend its inherent value, it is proposed to make increasing use of these data storage systems. The depositing of raw data is very much in keeping with the views of the genomics community and the reporting of next-gen sequencing results. These and other proposed changes will be discussed in this forum.

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