Keeping up with the bases: 'nextgen' approaches to proteomics

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A famous biochemist, Arthur Kornberg, in his book "For the Love of Enzymes" once said 'DNA and RNA are the script, but proteins are the actors'. Proteomics, the study of the actors, (whether in soliloquy or in crowd scenes) has terrific potential in diagnostics, in the analysis of new disease biomarkers, in understanding the fundamental ways by which the 'intent' of the genes is realised. At present, the global study of proteins (proteomics) is lagging behind our understanding of genomes and RNA, and without radical new technical approaches, taking the best of the analytical capability and coupling it to new methods of sample delivery, the gap is likely to widen. The challenges are several. First, a true global proteome analysis has to be able to deal with a highly complex mixture of proteins, some present in huge quantities, others at vanishingly low levels. This will require a degree of normalization, in which low abundance proteins are brought to the analytical step in sufficient amounts for analysis, and high abundant proteins are non-selectively sampled. Secondly, current proteomics is still predominantly based on prior digestion of proteins to multiple smaller peptides using an enzyme (trypsin) derived from the gut. This not only increases analyte complexity about 50 times but also conceals much of the subtlety of the protein world (just as a pile of bricks cannot inform about the structure of the the many building types and variants that could have been made from those bricks). A future solution should be based on protein-level analysis - architecture is less about the study of bricks than it is the exploration and celebration of the entire structures that the bricks are assembled to create. Finally, we deliver peptides slowly (1-4h per sample) by rather troublesome chromatography. Alternative approaches to protein-level delivery are required. I propose that we should plan to analyse a proteome without the complication of digestion or of chromatography. This poses new challenges, because we cannot expect the mass spectrometer to be able to analyse a whole proteome at once (it is just too complex). I therefore wish to devise an entirely new approach to proteome analysis based on delivery of a small number of proteins at any one time to the analytical platforms. The industrial collaborator has invented new types of genetically altered proteins ('Affimers', because they have a high affinity for selected target proteins) that are capable of selectively binding and fishing out a few proteins at a time. With appropriate analytical instrumentation, we should then be able to deliver the payload (proteins) in such a way that we can analyse them directly, capturing all of the complexity of the protein world - the architect's view. In the longer term, engineering solutions to payload delivery could make this the preferred approach to proteome analysis.