Methodologies for proteomic analysis. (a) Experimental workflow of common mass spectrometry (MS)-based proteomic approaches. Proteins from particular compartments or from whole-cell lysates may be separated using gel electrophoresis or chromatography. Individual fractions are subsequently digested, followed by MS of peptide mixtures. (b) Affinity-based proteomic analysis is generally applied to intact proteins. Antibodies with defined specificities may be arrayed on a glass slide or membrane followed by incubation with a lysate. Alternatively, with reverse phase protein arrays, lysates are spotted and incubated with individual antibodies that target a specific protein.