Within a decade proteomics has evolved from a fledgling discipline reserved for specialised laboratories, to a firm fixture in our standard omics arsenal used routinely by the research community. This stunning progress is due to many factors; the finishing of the genome projects provided major intellectual motivation and the development of better and much easier to use mass spectrometry (MS) instruments were technological drivers. What is even more remarkable is that this progress has been made despite leaving some main issues in proteomics unsolved. Besides these known boundaries, it also has revealed new frontiers and new interesting glimpses into the world beyond. This essay discusses some selected issues, but cannot necessarily be exhaustive or free of personal opinion.
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