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[email protected] EDITOR-IN-CHIEF
editorial
William S. Hancock Barnett Institute and Department of Chemistry Northeastern University 360 Huntington Avenue 341 Mugar Bldg. Boston, MA 02115 617-373-4881; Fax: 617-373-2855
[email protected] ASSOCIATE EDITORS
Joshua LaBaer Harvard Medical School
György Marko-Varga AstraZeneca and Lund University
EDITORIAL ADVISORY BOARD
Ruedi H. Aebersold Institute for Systems Biology
Leigh Anderson Large Scale Biology
Ettore Appella National Cancer Institute
Ronald Beavis Proteomic Solutions
Walter Blackstock Cellzome
Brian Chait The Rockefeller University
Patrick L. Coleman 3M
Catherine Fenselau University of Maryland
Daniel Figeys MDS Proteomics
Sam Hanash University of Michigan
Stanley Hefta Bristol-Myers Squibb
Donald F. Hunt University of Virginia
Barry L. Karger Northeastern University
Daniel C. Liebler University of Arizona
Lance Liotta National Cancer Institute
Matthias Mann University of Southern Denmark
Stephen A. Martin Applied Biosystems
Jeremy Nicholson Imperial College of London
Emanuel Petricoin Food and Drug Administration
J. Michael Ramsey Oak Ridge National Laboratory
Pier Giorgio Righetti
How Good Are We? t this point in the development of the proteomics field, I think we are all aware of the technical challenges that await the implementation of a successful proteomics program. It is clear that the field is moving quickly, with significant government and private funding in a wide range of countries, in both Europe and Asia, as well as the Americas. One aspect of this is an impressive array of publications announcing different technical solutions to current challenges in proteomics such as quantitation, the characterization of post-translational modifications such as phosphorylation and glycosylation, and the minimization of false positives and negatives in the interpretation of mass spectra. What is not clear in all of this activity, however, is which of the various approaches is the best and whether all laboratories are equally proficient in these complex technical measurements. In parallel developments in other areas, such as the environmental field, drug testing in the Olympics, and drug metabolism studies, there are national and international bodies that have laboratory certification programs and require these laboratories to analyze test samples and report results at international meetings. This has not been the practice in proteomics, but we see the beginnings of efforts in this direction. In the Association of Biochemical Research Facilities (ABRF) meeting, there has been a competition for several years in which many of the laboratories are encouraged to analyze a test sample and report their results at the meeting. This year the competition involved the determination of the site of phosphorylation of a peptide mixed in with a large amount of contaminating proteins. In a sense this was a simple exercise, which did not represent a complex proteomic sample. The phosphopeptide did not have to be generated by cleavage of a small amount of the corresponding protein, and the position was presumably 100% modified. This being the case, however, the meeting report noted that most laboratories were not able to carry out the determination and there was probably some issue with the stability of the test sample. This result reminds us of two points: such an exercise is very worthwhile, and because of the variable level of technical expertise in different laboratories, moreover, such a competition without 100% participation and standardization will merely reveal the tip of the iceberg. Another activity is beginning with the Human Proteome Organization (HUPO) and its efforts at coordinating international proteomics programs, such as the characterization of the blood and liver proteomes. As part of this effort, different laboratories are being recruited as reference laboratories for one or more of these activities. There is also an element of technology development as well as standardization of methodology reflecting the early stage of proteomics. Such an activity can also have the welcome benefit of developing comparison of capability between the laboratories. One can easily see the peril that proteomic studies produced in one laboratory will not be reproduced elsewhere in the world, leading to confusion about the size and variability of a given proteome, which may be confused with the biological variability of individual samples, differences in storage conditions, or even differences due to an individual population’s disease states. In conclusion, I support these two early efforts by ABRF and HUPO and encourage these organizations and others to come up with robust certification programs that allow for the worldwide effort in proteomics to be successful and of uniform value.
A
University of Verona
John T. Stults Biospect, Inc.
Peter Wagner Zyomyx
Keith Williams Proteome Systems
Qi-Chang Xia Shanghai Institute of Biochemistry
John R.Yates, III The Scripps Research Institute
© 2003 American Chemical Society
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