on 05-04-201604:52 AM - edited on 10-15-202112:01 PM by Closed Account
Adele Bourmaud1,2, Sebastien Gallien, Bruno Domon1,2 Proteomics Accepted manuscript online: 4 MAY 2016 03:36AM EST | DOI: 10.1002/pmic.201500543 Targeted mass spectrometry-based approaches are nowadays widely used for quantitative proteomics studies and more recently have been implemented on high resolution/accurate mass (HRAM) instruments resulting in a considerable performance improvement. More specifically, the parallel reaction monitoring technique (PRM) performed on quadrupole-Orbitrap mass spectrometers, leveraging the high resolution and trapping capabilities of the instrument, offers a clear advantage over the conventional selected reaction monitoring (SRM) measurements executed on triple quadrupole instruments. Analyses performed in HRAM mode allow for an improved discrimination between signals derived from analytes and those resulting from matrix interferences translating in the reliable quantification of low abundance components. The purpose of the study defines various implementation schemes of PRM, namely: i) exploratory experiments assessing the detectability of very large sets of peptides (100-1000), ii) wide-screen using (crude) internal standards obtain statistically meaningful (relative) quantitative analyses, and iii) precise/accurate quantification of limited number of analytes using calibrated internal standards. Each of the three implementation schemes require specific acquisition methods with defined parameters to appropriately control the acquisition during the actual peptide elution. This tutorial describes the different PRM approaches and discusses their benefits and limitations in terms of quantification performance and confidence in the identification of the analytes.