Reporting Protein Identification Data: The next Generation of Guidelines

doi:10.1074/mcp.E600005-MCP200

Editorial

Reporting Protein Identification Data

The next Generation of Guidelines

Ralph A. Bradshaw, Alma L. Burlingame, Steven Carr and Ruedi Aebersold

In June 2004, in response to a growing concern among both editorsand reviewers, we published a set of instructions to authors,developed in house by a committee chaired by Steve Carr, whichspelled out criteria for reporting protein identifications determinedby mass spectrometry. The overall response from the communityat large to this effort was quite favorable, and we were encouragedto expand on this document by soliciting broader input froma larger group of stakeholders with the view of fashioning auniversal set of guidelines that might be useful, in general,for publishers of journals reporting this type of data. Accordingly,with support from the American Society for Biochemistry andMolecular Biology (ASBMB) and the organizational skills of MikeBaldwin, including important input from Steve Carr, Ruedi Aebersold,and Al Burlingame, a two-day workshop was held in mid-May 2005in the Maison de la Chimie in Paris, France, that was attendedby 30 (of the $~$ 60 invited) scientists, engineers, bioinformaticians,and editors/publishers representing academia, research/governmentinstitutes, and the private sector (see below). This group reflectedan excellent cross-section of individuals involved in the developmentof mass spectrometry and its proteomic applications. The attendeesspent a day presenting/discussing the issues, ¹ and then, usingthe Carr guidelines as a point of departure, divided into foursubgroups, with each working through a section. The four rewritten(or, in some cases, new) sections were resynthesized into asingle document and were then subjected to further post-meetingediting. In mid-July the draft document was released and broadlydisseminated for public comment, suggestions, and criticism.In October, these were collated and returned to the originalParis groups for further editing. The final document was assembledin late January/early February 2006. In mid-February, the finalguidelines were aired and discussed at an open forum at theAssociation of Biomolecular Resource Facilities (ABRF) meetingin Long Beach, CA. They have been subsequently sent to the editorsof journals interested in this type of data.

The guidelines are now posted on the MCP website (http://www.mcponline.org)and have been officially adopted by the journal as the instructionsto authors for papers in this area. They eventually will beshifted to that part of the journal, but we felt initially thatit was appropriate to make them as visible as possible. At thesame time that the Paris guidelines were being developed, MCPincorporated a mechanism for evaluating papers for their compliancewith the guidelines (initially the Carr guidelines but now thosedeveloped in Paris) that inserts an independent evaluation inthe review process. A simplified outline of the guidelines inthe form of a checklist is used and will be returned to authorsby the Associate Editor that documents any areas of deficiency.The checklist will also be sent to the reviewers, along withthe submitted materials to facilitate the review and to makecompliance with the guidelines more consistent. Additional commentsalso may be added to help clarify the problems detected. Thisassessment is not considered to be a review, and unless thedeficiencies are deemed to be so great by the Associate Editor,after receiving the checker’s report, that in the AssociateEditor’s opinion the manuscript cannot be appropriatelyreviewed until the deficiencies are corrected, they will bereturned along with the usual reviewer critiques, and the complianceissues can be dealt with at the time any other corrections/changesare made.

Our initial experiences with this independent evaluation havebeen quite favorable, and we feel that it is already havingthe desired effect of bringing papers reporting protein identificationsinto a more consistent form. However, the main goal of theseefforts was to address the problem of misidentifications andsecure the integrity of the scientific literature. To this endwe naturally hope that authors, reviewers and editors alikewill find these guidelines useful and worthy of serious consideration.We also appreciate that science is a dynamic process and thattoday’s guidelines can become tomorrow’s burdens.Therefore, we will be watchful for advances in technology thatmake any part of these guidelines obsolete and will welcomesuggestions and comments that will aid us in keeping them current.

We would also like to thank the many people who contributedfreely of their time to make this goal a reality. We particularlythank Alexey Nesvizhskii, Robert Chalkley, and Karl Clauserfor their help in preparing the original Carr document, to MikeBaldwin and all the participants at the Paris meeting, and tothe ASBMB for their financial and intellectual support.

LIST OF PARTICIPANTS IN THE PARIS MEETING

Phil Andrews, University of Michigan Medical School

Rolf Apweiler, European Bioinformatics Institute

Kathy Aschheim, Nature Biotechnology

David Baker, University of Washington

Ronald Beavis, Beavis Informatics, Ltd.

Leo Bonilla, Harvard/Partners Center for Genetics and Genomics

Ralph A. Bradshaw, University of California, Irvine

Alma L. Burlingame, University of California, San Francisco

Steve Carr, ² Broad Institute of MIT and Harvard

Robert Chalkey, University of California, San Francisco

Karl R. Clauser, Broad Institute of MIT and Harvard.