Computational Mass Spectrometry–Based Proteomics
Figure 3
Mass spectrometry–based measurements.
(a) Sample processing. Label-free quantification requires minimal sample manipulation, and acquires spectra from each sample in a separate mass spectrometry run. Label-based quantification varies in the timing and type of the labeling steps, but always simultaneously profiles two or more biological samples within a run. (b) Global label-free workflows achieve relative quantification by comparing counts of MS/MS spectra, or intensities of MS peaks between runs. Global label-based workflows compare intensities of reporter MS/MS fragments (iTRAQ) or MS peaks (SILAC, synthetic peptides). (c) Targeted workflows are an alternative to global quantification. They are most sensitive, but require an a priori knowledge of the proteins of interest, and of the technological characteristics of their peptides. Label-free targeted experiments compare intensities of transitions between runs, and label-based experiments within a run.