In Praise of Toolmakers he term “proteomics” was first used in print in 1995,1 coinciding with the beginning of the exponential growth of this new postgenomic area of research. Rapid global expansion was based on the realization2-4 that automated comparison of MS measurements of peptides to protein sequences available in databases could provide rapid and automated identification of proteins in laboratory samples. This commentary seeks to point out that the greatly expanded market produced by the growth of MS-based proteomic studies has led to novel and significantly improved MS instrumentation with increased sensitivity, expanded functions, robust integration of HPLC, and, most important, highly automated computer control to facilitate the analysis of the very complex samples generated in many of these workflows. In particular, many new types of tandem and hybrid instruments have been commercialized to provide low- and high-resolution MS/MS spectra and multiple reaction monitoring (known as MRM) measurements. These improvements also benefit investigators who work with small molecules and other kinds of biopolymers and provide the foundation for further developments in ion chemistry and ion activation research. Because the simultaneous examination of many proteins generates complex mixtures of peptides, separation science has also been highly stimulated. The precedent proteomic technique, 2DE, has seen an expanded market and significantly improved technology, including the commercial availability of robust and standardized gradient gels, the development of fluorescent dye tags that allow direct quantitative comparison of multiple samples on one gel, longer immobilized pH gradient (IPG) strips and narrow-range IPG strips, and the commercial development of computer programs to digitize, align, and quantify protein patterns on gel arrays. Interest in gel-free proteomics has catalyzed development of novel multistage HPLC separation procedures for peptides and proteins, as well as commercially available variations of new solution and capillary isoelectric focusing devices. Capillary and nanoflow HPLC, in particular, have become more robust. The recent introduction of commercial LC instrumentation that operates in the ultra-high-pressure regime and the development of new column stationary phases have increased the
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power of LC for the separation of complex proteomic (and other) mixtures. The third leg of the proteomics stool is, of course, bioinformatics. Many bioinformatics challenges in proteomics, such as recognition and calculation of isotope clusters and chargestate assignment, are traditional MS problems finding new application in proteomics, but data volume, high-throughput workflows, and the rich variety of bioinformatics data resources have required significant innovation. Promising work is under way on the development of label-free approaches for semiquantitative comparisons of samples in LC/MS-based workflows. The organization of proteins, once identified, into functional classes and pathways provides a foundation for systems biology, unifying the insights of genomics, transcriptomics, and proteomics in one framework. We can also ask how the proteomic revolution and its rapidly expanding analytical capabilities have changed biological research. Here, the focus for many investigators has moved to proteins as the active agents of genes. Because many proteins are viewed simultaneously, discovery experiments are enabled. At the same time, more effort can be expended to address protein function and protein networks, because less effort is required to address protein sequences. Temporal and spatial pancellular dynamics are under examination as proteomics opens new doors in cell biology as well as in the search for clinical biomarkers. Analytical chemistry has provided the foundation and the catalyst for this important new area of science. Three cheers for the MS designers, the separation scientists, the bioinformatics community, and the agencies that see fit to fund their developments and inventions. CATHERINE FENSELAU University of Maryland
References (1) Wasinger, V. C.; et al. Electrophoresis 1995, 16, 1090–1094. (2) Henzel, W. J.; et al. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 5011– 5015. (3) Eng, J. K.; McCormack, A. L.; Yates, J. R. J. Am. Soc. Mass Spectrom. 1994, 5, 976–989. (4) Shevchenko, A.; et al. Anal. Chem. 1996, 68, 850–858.
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