Technological innovation revisited.

As the journal moves into its 10th year of publication, it (really those charged with its editorial well-being) continues to monitor developments in the field of proteomics, including activities in the related fields of genomics, transcriptomics, and metabolomics, with the view of introducing appropriate changes to accommodate them. This includes keeping our clinical and mass spectrometric identification guidelines current and our topic coverage abreast of the rapid changes in this dynamic area of research. In the former category, we have in the past 6 months introduced updated guidelines for peptide/protein/post-translational modification identifications that include the deposition of the raw data behind these analyses in public repositories in addition to the information we have always required. We are still concerned about the management of this information, and the journal held a workshop in Boston this past July, to which a couple of dozen experts were invited, to further consider the best way to deal with this information and its accessibility for potential interrogation by reviewers and the community at large. At the same time, the assembled group reviewed the still very difficult issue of the accuracy of reported locations of post-translational modifications in peptides based on tandem mass spectrometry and how best to determine the reliability of an author’s assignments. A “white paper” reporting the conclusions of these discussions will be published by the journal in the next few months. A similar review of our clinical guidelines that were adopted nearly 2 years ago is scheduled for next spring to assess their effectiveness and to consider what changes, if any, are warranted. The issue of topic coverage has been one of the journal’s concerns since its founding. Indeed, when the journal first began, we requested our reviewers to opine on whether a given manuscript fell into the general scope of proteomics. There was then, and still is, divided opinion on this subject, and for the most part, we have tried “to paint with a broad brush,” even occasionally including articles from other -omics areas. We also recognized early on that proteomics experimentation was highly dependent on technological advancement. It is, in this regard, perhaps useful to note that proteomics exemplifies particularly well the concept of a “paradigm shift,” as spelled out by Kuhn (1), in which intellectual progress is viewed as making quantum jumps as opposed to developing by a linear progression (described as “developmentby-accumulation”). In this model, science (and hence scientists) are viewed as working within an established framework of ideas that are “defined” by rules and conventions, and only when sufficient anomalies have arisen that cannot be explained or “answered using the tools of the existing model” does a new paradigm arise, put forward by a few adventurous (and highly creative) individuals, who begin by inventing new rules and conventions that ultimately cause the collapse of the old paradigm and the appearance of a new one (2). Although proteomics can be defined in a variety of ways, it is invariably related to the introduction of two-dimensional gels (3, 4) and the invention of fast atom bombardment (liquid secondary ion mass spectrometry) (5, 6), MALDI (7, 8), and ESI (9) as three radical new ways to inject protonated or deprotonated polar molecules into the gas phase for analysis by mass spectrometry. These revolutionary ionization methods made mass spectrometry applicable to macromolecules and, coupled with the determination of the human genome (and many genomes subsequently) (10, 11), formed the paradigm-shifting technologies (or technologically based products) that were essential for the proteomics advances that followed. They also generated the need for new methodology for improving sample separation, sensitivity, dynamic range, and high throughput analyses to name a few and, perhaps most important of all, required improved software to analyze, sort, and interpret the vast of amount of information that they can generate. A few years ago, we consolidated our types of original research-related contributions into one omnibus category, making the principal criterion for acceptance be “that the article must make a significant contribution to proteomics.” It was not our intention to exclude technologically based articles, but somehow this idea seems to have crept into the understanding of reviewers (then later authors). We also experimented with data set papers but ultimately required that articles of this type have sufficient biological relevance or new insight that they became indistinguishable from other research contributions. We now think that perhaps the field has evolved sufficiently that it is time to return to those ideas. The importance of technological advances and software development has never been stronger, and the growth in public databases and the ability to interrogate information placed in them suggest to us that revisiting both of these “old” categories again is indeed timely. This is also in keeping with our new requirements for the deposition of raw data from large scale mass spectrometric analyses. To complement this change, we are planning to introduce a series of review articles that will address both biological issues (germane to proteomics anal‡ To whom correspondence should be addressed: University of California, 600 16th St., Genentech Hall, Rm. N472, Box 2240, San Francisco, CA 94158-2240. Tel.: 415-476-3813; E-mail: [email protected]. Published, MCP Papers in Press, October 13, 2010, DOI 10.1074/ mcp.E110.005447 Editorial