For the past 10 years – indeed, from its inception – Molecular & Cellular Proteomics, the American Society for Biochemistry and Molecular Biology’s only home-grown journal, has enjoyed an almost unique leadership position in the development of its field and the role that proteomics is playing in helping unravel the mysteries of biological systems.
Proteomics, which in general terms involves using unbiased methodology to look at proteins and the entities with which they interact as ensembles (or unfractionated mixtures) rather than as individual molecules, clearly began to emerge in the ’70s. The introduction of key mass spectrometric and array technologies greatly accelerated its development and the availability of genomic information aided it immensely. These enablers came rapidly to a head in the ’90s, and thus the launch of MCP in the summer of 2001 was timely in helping usher in the era of proteomics.
As with any paradigm shift – and proteomics clearly qualifies for such a designation (1) – there were exaggerated hopes, promises and predictions for breakthroughs that would materially change our understanding of human biology and improve our existence and well-being. Not surprisingly, much of this has not come to pass, and proteomics has not yet proved to be quite the panacea that was predicted, for example, in revolutionizing the practice of human medicine.
But to focus on these apparent shortcomings is looking through a glass darkly and ignores the very considerable successes that have occurred. Among other major advances, we now appreciate the extent to which virtually all proteins interact with multiple partners and the fact that protein post-translational modifications are orders of magnitude more extensive than we ever realized. Such significant shifts in basic biological concepts rarely have occurred as quickly as those of the past several years and would not have been possible without proteomic technology. Practical applications also have not been neglected.
Detractors of proteomics are wont to point out that very few new diagnostics have come out of proteomic biomarker identification analyses. While that is true, it is more a failure of germane research and development programs than proteomics. Indeed, literally thousands of biomarkers have been reported for a host of pathologies (and many of these in MCP), but they await validation before they can reach the marketplace.
Validation, however, is not the role or job of proteomics, and proteomics should not be blamed for the painfully slow movement of potential therapeutics and diagnostics through the pipeline. It is far too early to know what the long-term contributions of proteomics will be, but it is a very pessimistic individual who does not think that those contributions will be considerable.
MCP was founded on the principle that it would be proactive in advancing this exciting field, and it has been good to its promise. From the outset, it focused on the quality of data submitted to it and over several years developed guidelines for reporting peptide and protein identifications using mass spectrometry and clinically relevant data to insure that this information was correct and reproducible. Both guidelines are viewed widely as the standards in the field.
Indeed, by a variety of metrics and peer recognition, MCP is arguably the leading journal in this area and is quite deserving of its position as one of the 100 most influential journals in biology (2). However, it is important to remember that the successes of the journal are the result of the efforts of a large number of people, starting with the associate editors and the members of the editorial board and including all the authors and scientists who have chosen to publish their outstanding work in the journal. The content of the journal is, in the final analysis, what dictates its quality. It has had 10 excellent years in this regard, and we look forward to the next decade and even better things.
As part of our 10th anniversary celebration, the editors of MCP are planning to introduce some new features and policies that we feel will not only maintain our tradition of excellence but also keep us fresh and innovative. One such feature is the introduction of MCP-sponsored lectures in germane meetings and symposia, which we initiated in August at the 10th International Symposium on Mass Spectrometry in the Health and Life Sciences in San Francisco and continued in September at the 10th HUPO Annual World Congress in Geneva. The organizers of the meeting selected the lecturers in each case, and two of the leading practitioners of the proteomic art kicked off this program: Matthias Mann and Ruedi Aebersold.
Matthias Mann received his bachelor’s and master’s degrees at the University of Gottingen and his doctoral degree from Yale University under the direction of John Fenn, who received the Nobel Prize for chemistry for the development of electrospray ionization (to which Mann contributed). Mann did postdoctoral work at the University of Southern Denmark in Odense with Peter Roepstorff and held a professorship at the same university subsequently.
In between these appointments, he was a group leader at the European Molecular Biology Laboratory in Heidelberg. During his stay at that institution, he was instrumental in developing high-throughput protein identifications by mass spectrometry that were key to the advance of proteomics. In 2005, he became a director at the Max Planck Institute of Biochemistry in Martinsried (outside Munich), and he also holds an appointment at the University of Copenhagen.
Mann is an acknowledged leader and pioneer in the development of mass-spectrometric-based proteomics and has received numerous prizes and recognition for his extensive achievements. He and his co-workers have developed many important analytical techniques, including stable isotope labeling with amino acids in cell culture (SILAC labeling) (published in MCP) for quantifying MS data (3). He is particularly known for large-scale identifications of proteins and PTMs and the analysis of important complexes and samples of clinical significance. He has published more than 400 research articles (38 of which have appeared in MCP); he is also a member of the MCP editorial board. His keynote MCP lecture for the International Symposium on Mass Spectrometry in the Health and Life Sciences was titled “Technology and Applications of Deep Proteome Sequencing” and covered new developments in mass-spectrometric-based technologies and how these improvements are placing proteomics on a par with genomics in terms of sample coverage.
Ruedi Aebersold received his formal training at the Biocenter at the University of Basel and did postdoctoral research at the California Institute of Technology with Lee Hood. He then held academic appointments at the University of British Columbia and the University of Washington, where he and his colleagues worked on a wide variety of proteins and made major contributions to their micro-characterization.
In 2000, Aebersold co-founded the Institute for Systems Biology in Seattle, which has been a leading proponent of the application of proteomic methods and techniques to understanding cell biology at an integrated level. In 2004, he returned to his native Switzerland as a professor at the Swiss Federal Institute of Technology Zurich and the University of Zurich to continue these efforts.
He was one of the earliest investigators to appreciate the importance and power of mass
spectrometry in analyzing peptide and protein samples and has been one of the pioneers in the use of this technology.
Aebersold also has received substantial recognition and numerous awards, including the ASBMB Herbert A. Sober Award in 2010, for his studies, responsibilities and associations. He serves on seven editorial boards and was one of the founding associate editors of MCP (and has published in the journal 50 of his more than 500 contributions). His lecture at the 10th HUPO Congress is titled “The Organization of the Proteome in Time and Space” and reflects his continued interest in expanding our appreciation of living systems by better understanding the dynamics of the proteome.
Both Mann and Aebersold are prominent members of a small cadre of innovators who have birthed the field of proteomics and are now driving its still largely undeveloped potential to ask (and answer) increasingly complex questions. They perfectly represent the power of mass spectrometry and related technologies to eventually make good on the early promises of proteomics (and the other omic sciences) to make significant inroads into the pressing problems associated with health, energy, food supply and the environment. As such, they are ideally suited to initiate the MCP lecture program. We look forward to this tradition continuing at other meetings and symposia.
- 1. Bradshaw, R. A. and Burlingame, A. L. (2010). Technological innovation revisited, Mol Cell Proteomics 9, 2335 – 2336
- 2. Special Library Association’s 2009 ranking of the top 100 journals in biology and Medicine: http://units.sla.org/division/dbio/publications/resources/dbio100.html
- 3. Ong, S. E.; Blagoev, B., Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; and Mann, M. (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1, 376 – 386
Ralph A. Bradshaw (email@example.com) and Al L. Burlingame (firstname.lastname@example.org) are co-editors of Molecular & Cellular Proteomics.