Targeted Quantification of Phosphopeptides by Parallel Reaction Monitoring (PRM)

Abstract

Parallel reaction monitoring (PRM) is a liquid chromatography–mass spectrometry (LC-MS)-based targeted peptide/protein quantification method that was initially implemented for Orbitrap mass spectrometers. Here, we describe detailed workflows that utilize the freely available MaxQuant and Skyline software packages to target peptides of interest, primarily focusing on phosphopeptides.