Based on rapid methodological developments in 2009, last year we selected targeted proteomics analysis by mass spectrometry as a Method to Watch. Progress in 2010 continued at a quickening pace.

The targeted proteomics approach differs fundamentally from the more familiar 'shotgun' approach in which the spectra generated from all detectable proteins in a sample are interpreted by database searching. In a targeted analysis, the mass spectrometer is programmed to analyze a preselected group of proteins. This can be achieved using a technology called selected reaction monitoring (SRM; also referred to as multiple reaction monitoring, MRM), whereby assays are developed on a triple quadrupole instrument to detect fragment-ion signals arising from unique diagnostic peptides representing each of the targeted proteins.

Proteins are detected with high sensitivity and reproducibility via targeted proteomics.

The SRM approach has proved to be highly sensitive, quantitatively accurate and highly reproducible. Compared to shotgun proteomics (still largely the domain of experts), protein detection is relatively rapid and straightforward with SRM. Though not yet quite as sensitive as immunological assays, SRM has the clear edge for multiplexed detection.

The main bottleneck to applying this technology on a broad scale has been the difficulty of generating high-quality SRM assays. Over the last couple of years, methods for selecting appropriate diagnostic peptides and for generating SRM assays in high throughput using crude peptides have been developed. These developments have allowed Ruedi Aebersold's group to greatly expand their SRM Atlas database (Nat. Methods 5, 913–914; 2008); as a result of an intensified joint effort with Rob Moritz, this resource will soon feature SRM assays for about 95% of proteins from humans and yeast, and about 55% of mouse proteins.

As the availability of SRM assays grows, so will the biological applications of the technology. Many researchers see great potential in applying SRM for biomarker validation and systems biology studies. Recently, SRM was used to validate computationally predicted microRNA targets in worms (Nat. Methods 7, 837–842; 2010). This work likely represents just a taste of interesting applications to come.