Figure 2: Mass spectrometry approaches for the identification and quantitation of MHC peptides. (A) Multiple reaction monitoring (MRM); during MRM-LCMS, a known peptide(s) of interest is detected based on its precursor mass and characteristic daughter ions generated upon fragmentation. Incorporation of an isotopically labeled internal peptide standard, allows absolute quantitation in the same experiment. (B) LC-MS/MS analysis; only the most abundant precursor ions are selected for fragmentation. Although this technique is not as sensitive as MRM analysis, it does not require any prior knowledge of the peptide of interest, providing a tool for the identification of novel sequences. (C) SWATH-MS; all analytes entering the mass spectrometer are subjected to MS/MS based fragmentation, even those present in low abundance. Postacquisition extraction of peptide precursor mass and fragmentation information allow the detection of peptides of interest.