Probing cellular complexity with proteomics

The pace of genome sequencing means that many if not all newly discovered genes have either no known function, or functions that, at best, are poorly described. The classical approach to detailed annotation of individual genes cannot deal with the flood of new sequences. Increasingly, high-throughput global approaches are being used, where changes in expression of many genes are measured in parallel. Proteomics is one such approach. At present, a snapshot of all protein levels in a cell is taken indirectly by looking at the mRNA (the transcriptome). Making the comparable measurement at the protein level is technically difficult, and unlikely to be competitive with mRNA-based approaches. Correlation of the abundance of the mRNA and cognate protein is, however, far from simple. Nonetheless, proteomics has a role in more focused studies, especially in the study of protein complexes, where the direct isolation of complexes, combined with mass spectrometry, has proved to be a very powerful tool. This approach has been termed 'cell map proteomics' and offers a rapid route to studying protein complexes and higher order structures.