Mass spectrometry-based quantification

ObjectiveThis review describes the most common methods currently used for mass spectrometry‐based quantification in proteomic applications.Design and methodsQuantification 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.ResultsA number of commercial labeling reagents are now available and each of these are described along with their strengths and limitations.ConclusionsThe choice of method will ultimately depend, not just on financial considerations, but also on the context of the experiment.

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► Current approaches for mass spectrometry-based quantification of proteins are reviewed.
► Labeled and unlabeled approaches are described.
► Labeled approaches include chemical, metabolic, synthetic and proteolytic labeling.
► Unlabeled approaches include spectral counting and ion intensity based approaches.