Proteins can be detected with very high sensitivity and reproducibility through targeted proteomics approaches.

In a typical 'shotgun' proteomic analysis, a mixture of proteins is digested into peptides, fractionated and analyzed by mass spectrometry. This in theory could lead to the discovery of all proteins in the sample, though in practice this is extremely challenging and requires huge resources. But for many types of experiments, the researcher does not necessarily want to discover new proteins but instead is interested in following what happens to a relatively small number of proteins under different conditions.

For such experiments, targeted approaches such as selected reaction monitoring (SRM; or multiple reaction monitoring, MRM, as it is also commonly known) offer much higher sensitivity and much greater speed of analysis. Developing and validating SRM assays is an extensive process, but once generated for a particular protein, this mass spectrometric assay can be deployed for the accurate identification and quantification of that protein across biological samples.

Though the SRM approach has been around for many years, it has only recently been gaining traction in the field of proteomics. Ruedi Aebersold's group has been particularly influential in pushing the technology forward. This year, they showed that SRM could be used to detect expressed proteins over a wide dynamic range, down to the unprecedented level of fewer than 50 copies per cell (Cell 138, 795–806, 2009). In this issue, the Aebersold group also demonstrated that cheaply synthesized crude peptides can be used for the high-throughput generation of SRM assays (Nat. Methods 7, 43–43, 2010). Additionally, a multilaboratory study showed that SRM assays are transferrable and reproducible across laboratories (Nat. Biotechnol. 27, 633–641, 2009).

It will take a long time to build up a database of SRM assays for whole proteomes, but we are likely to see rapid growth in this area, which will facilitate high-throughput and highly sensitive protein detection for a wide variety of experiments.