The 'SILAC mouse': metabolic isotope labeling now allows quantitative comparison of the proteomes of knockout mice.

Mass spectrometry has made protein identification fairly routine and is now widely used in proteomic studies. But to really understand the biology of complex systems, one also needs information about protein expression levels. Unfortunately, mass spectrometry is not inherently quantitative.

Therefore, over the last decade, proteomics researchers have devised a series of stable-isotope labeling strategies to obtain quantitative information. These methods have been touted for investigating the effects of knockdown, of an inhibitor, or of the environment on a proteome; for comparing two disease states; for determining the stoichiometry of proteins in a large complex; or even for monitoring changes to a proteome over time.

Made possible also by recent advances in instrumentation and bioinformatics analysis, several noteworthy proteomics studies have been reported over just the last year, in particular using metabolic labeling techniques such as the SILAC (stable isotope labeling by amino acids in cell culture) method invented by Matthias Mann's group in 2002. In 2008, Mann's group and others showed, to give a few examples, that SILAC can be used to isotope-label a whole mouse, investigate the dynamics of phosphorylation across the cell cycle, study the effects of microRNA on cellular proteomes, and compare the proteomes of haploid and diploid yeast.

Absolute quantification of protein levels, however, can only be achieved by spiking a digested proteomic sample with known amounts of synthetic, isotope-labeled peptides, a concept first introduced by Steven Gygi's group in 2003. However, until isotope-labeled proteotypic peptides (those most likely to be consistently detected by the finicky mass spectrometer) representing all proteins are available, absolute quantification on a proteomic scale is a far-away dream.

In the near future, look for further exciting applications using metabolic isotope labeling. The stage is now set for researchers to use mass spectrometry to answer challenging biological questions on a proteomic scale.