Fig. 1.

Experimental methods for analysis of proteomic alterations. (A) Gel-based and gel-free proteomics workflows. (B) Methods for targeted mass spectrometry analysis. Selected reaction monitoring (SRM) commonly relies on a triple-quadruple mass spectrometry-instrument. Specific peptide/fragment mass pairs (transitions) are selected and generated with quadrupole mass filters (Q1–Q3). During a targeted experiment the mass-spectrometer can cycle though several transitions to allow for multiplexing. Parallel reaction monitoring (PRM) is a related technology, which relies on a high resolution fragment mass-analyzer such as an Orbitrap rather than a quadruple. With this, all fragment ions of the selected peptides can be identified and quantified in parallel. (C) Mass spectrometry-based phospho-profiling workflow.