Our Method of the Year 2012 features mass spectrometry as applied to one area, targeted proteome analysis, but this versatile molecular 'weighing' technology is well suited to address a variety of scientific questions across disciplines. One interesting area to watch is the application of mass spectrometry to detect and characterize proteins and protein complexes in their intact state.

Most of the time, mass spectrometry analyses of proteins are performed using a 'shotgun' strategy: researchers wanting to identify, quantify and characterize proteins in a sample first snip them into peptides, which are more readily detected by the instrument than are intact proteins. Though the shotgun approach has met with wide success for high-throughput proteome profiling, much biological information is lost in the process. Proteins often contain patterns of multiple post-translational modifications that affect how they function, but when the proteins are chopped up into peptides, these patterns become difficult to interpret. Further, proteins rarely act in isolation; rather, they carry out biological processes by interacting with other proteins and other molecules in the cell. Such information is also lost in a typical shotgun approach.

But by using unique mass spectrometry methods to detect and characterize intact proteins and protein complexes, valuable information providing clues as to a protein's function is retained. Proteins are gently ionized into the gas phase, which preserves their native three-dimensional structures; under the right conditions, even large, noncovalently bound, soluble and membrane-protein complexes can be observed intact by mass spectrometry.

The application of mass spectrometry to detect and characterize large, intact protein complexes (such as the yeast 20S proteasome, depicted here) seems likely to grow.

To date, however, mass spectrometry analysis of intact protein complexes has required highly specialized instrumentation and has therefore been limited to a handful of expert labs. But new developments in 2012 (R.J. Rose et al., Nat. Methods 9, 1084–1086, 2012), extending the use of the popular and powerful Orbitrap mass analyzer to detect large intact protein complexes with unprecedented sensitivity, may help bring the technology to a much broader swath of researchers. It will be particularly interesting to watch whether the technology can be merged with advanced 'top down' proteomics approaches (J.C. Tran et al., Nature 480, 254–258, 2011)—which seek to profile intact proteins and their post-translational modifications in high throughput—to allow detailed characterization of intact protein complexes on a proteome scale (P.D. Compton and N.L. Kelleher, Nat. Methods 9, 1065–1066, 2012).