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The recent development of hybrid mass spectrometers with high resolution and accurate mass capabilities has opened new avenues in quantitative proteomics. A systematic study was performed to assess the quantification performances of a novel quadrupole-Orbitrap instrument operated in MS/MS mode (parallel reaction monitoring). It included the analyses of 35 isotopically labeled peptides spiked in urine samples to establish their dilution curves. The results were evaluated by replicating the analyses on a triple quadrupole instrument operated in selected reaction monitoring (SRM; often referred as multiple reaction monitoring, MRM) mode to assess and compare the gain in selectivity resulting from high resolution fragment ion analysis. The high resolving power dramatically increased the selectivity of measurements by separating ions of interest from interferences, which occurred in several cases, and thus improved the quantification performance. In addition, an experiment to assess the "co-habitation" of fragment ions in specific regions of the LC-MS/MS spectral space of a complex proteome digest was carried out. The study included the evaluation of the fragmentation patterns acquired under various experimental conditions (i.e., quadrupole isolation windows and Orbitrap resolving powers) for more than 200 peptides, which provided an experimental baseline to guide the development of methods for parallel reaction monitoring acquisition. This article is part of a Special Issue entitled: From protein structures to clinical applications., (Copyright © 2012. Published by Elsevier B.V.)