Mass spectrometry-based quantification.

OBJECTIVE This review describes the most common methods currently used for mass spectrometry-based quantification in proteomic applications. DESIGN AND METHODS Quantification can be performed using either labeled or unlabeled approaches. Labeled approaches rely on mass-tagging of peptide reference standards either by direct synthesis or through chemical or metabolic means. Following labeling, samples are pooled and analyzed as one, thereby circumventing any potential error that could result from run-to-run variability. Unlabeled approaches rely on run-to-run comparisons between test and reference samples and assume a highly reproducible separation and similar sample compositions. RESULTS A number of commercial labeling reagents are now available and each of these are described along with their strengths and limitations. CONCLUSIONS The choice of method will ultimately depend, not just on financial considerations, but also on the context of the experiment.