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Mission Statement

Molecular & Cellular Proteomics – A Mission Statement

The accelerating determination of genome sequences and their interpretation (genomics) has brought with it one of the most daunting challenges to modern bioscience – the concomitant determination of the structure, function and expression of all of the corresponding proteins that are encoded therein. The magnitude of this task, even for a simple prokaryotic species, is staggering and that pales by comparison to eukaryotic examples. The problem comes in many parts ranging from protein isolation and identification to structure determination, protein/protein interactions and gene expression. and the solutions will embrace both existing technologies and methods yet to be developed. Thus this rapidly expanding field of proteomics, a term coined in an obvious parallel to genomics, is both an extension of traditional biochemistry and at the same time a new and exciting field. Moreover, the magnitude of this effort will produce amounts of data that will dwarf previous outputs and poses severe problems in its own right. The storage, analysis and manipulation of this information, already well recognized from the genome studies, has spawned a related field generally termed bioinformatics. In fact, these data sets will drive discovery research that is unparalleled in the history of bioscience and will likely eclipse, at least in the early stages, hypothesis driven experimentation. The management of research databases is not a new phenomenon but the size of the task will require new and innovative approaches here as well.

Since it can be (and has been) argued that such an understanding of protein structure and function has been the focus of biochemical research for the past 50 years or more (admittedly arbitrarily dated), it is reasonable to ask why, all of a sudden, there is such an increased interest? Where does the "sizzle" come from? The answer lies in the appreciation that substantial amounts of every genome examined to date, including the draft of the human genome, reveal protein sequences for which there are no structural or functional correlates and therefore represent fundamentally unknown entities. Estimates of the number of these "new" proteins vary, but it is certainly a daunting figure. It is understanding of how the structure and function of these proteins and their post-ribosomal modifications allow them to do what they do, who or what they interact with, and how they contribute to life processes that really lies at the heart of proteomics.

It is also noteworthy that the interest in proteomics has been driven by rapid developments in supporting technology. The "molecular biology revolution", which moved into high gear in the last quarter of the 20th Century was essential to provide us with today’s tools for the facile manipulation of proteins but these have also been paralleled with an ever increasingly sensitivity in more standard techniques and the rapid and impressive advances in the determination of three-dimensional structures. Also of more recent times has been the maturing of mass spectrometry as a more versatile methodology and the development of combinatorial chemistry (arrays of various sorts), which has the capacity to allow investigation of much broader responses in its different applications. Thus, not only is the puzzle defined (the determination of the gene sequences of so many unknown proteins) but the techniques by which to solve the complexities of their structure, function and expression are also in hand, not only at an individual level, but also in the context of their cellular milieus.

The scope of the journal, which is reflected in the title that has been selected, will be purposely broad. It will be open to contributions that describe the structural and functional properties of proteins and their expression, particularly with respect to the developmental time courses of the organism of which they are a part. Emphasis will be placed on determining how the presence or absence of proteins affects biological responses and how the interaction of proteins with germane cellular partners allows them to function. Thus, the focus clearly will be on both structural and functional aspects of proteins. However, as noted, technological advances have an important role in a field that is still clearly being formulated and significant advances in methodology would be deemed to be appropriate subject matter too

The inclusion of array technologies that measure changes in mRNA levels (as opposed to other arrays) can well be viewed as the interface between genomics and proteomics. However, the important predictive value of this information with respect to subsequent changes in expression of the proteins themselves suggests that this area of investigation also falls within the proposed scope of the journal.

It is also important to recognize that a significant part of the work on proteomics for the foreseeable future will reflect calculations and/or predictions as opposed to experimental data. This, of course, is particularly true for those aspects of bioinformatics that address needs in proteomics.

It is inherent both in the scope and the types of experimentation that will be the principle basis for the studies reported in this journal that they will generate substantive supporting databases. This information will be welcomed as appropriate supplemental material to the electronic version of the journal where space is essentially unlimited. The submission and publication of this information should, of course, be justified as supporting the main theme and/or interpretations of the paper, but it will be otherwise encouraged to the extent that it will be of value to other workers in the field. We will accept such information both as an appendix to a research paper and as papers primarily composed of a database (accompanied by a two-page summary explaining its significance. The journal will also establish hyperlinks with all germane databases that support proteomics so that the readership will be able to move facilely between the journal and these compendia. The management of compilations and the interaction with existing databases will be ongoing priority and will be constantly updated through the advice of a Database Management Committee, appointed to advise the Editors.

In summary, Molecular and Cellular Proteomics will publish three types of original articles: research papers, database articles and technology development articles. Mini-reviews and articles discussing important unresolved issues (perspective articles), as invited contributions, will also be published. Suggestions for appropriate topics will be welcome. Letters to the editor dealing with material published in MCP will be published at the discretion of the Editors.