Advances in higher order multiplexing techniques in proteomics

Proteomics by mass spectrometry (MS) allows the large-scale identification and quantitation of the cellular proteins in a given biological context. Systems biology studies from proteomics data are largely limited by the accuracy and coverage of quantitative proteomics along with missing values. Toward this end, statistically robust biological observations are required, comprising multiple replicates, preferably with little technical variations. Multiplexed labeling techniques in proteomics allow quantitative comparisons of several biological samples or conditions. In this focused Review, we discuss an emerging technique called higher order multiplexing or enhanced multiplexing, a unique combination of traditional MS1- and MS2-based quantitative proteomics methods that allows for expanding the multiplexing capability of MS methods to save valuable instrument time, achieve statistical robustness, enhance coverage and quantitation accuracy, and reduce the run-to-run variability. We discuss the various innova...