Hares and tortoises: the high- versus low-throughput proteomic race

The analysis of the proteome can be undertaken with parallel, high-throughput techniques or those that analyze proteins in a serial, one-at-a-time manner. The former include 2-D gels and shotgun MS/MS; the latter includes libraries containing fusion proteins (GST, green fluorescent protein, TAP-tag and others) that are engineered onto each protein in a proteome and then studied one by one. In this review, we explore the progress that these scientifically contrasting paradigms have made in measuring protein abundance, half-life, post-translational modifications, localization in cells and tissues and in protein membership of complexes, pathways and networks. We find that our understanding of the yeast proteome has been furthered more substantially by the slower "tortoise techniques" than the "high-throughput hares". A number of aspects of the human proteome are also likely to be elucidated most accurately with low-throughput approaches. However, the high-throughput techniques are expected to remain crucial for comparative analyses and most studies of proteome dynamics. This review also briefly explores how electrophoretic separations can continue to support the field of proteomics.