on 08-10-201207:03 AM - edited on 10-15-202106:12 AM by Closed Account
Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ. Mol Cell Proteomics. 2012 Nov;11(11):1475-88. Selected reaction monitoring (SRM) on a triple quadrupole (QqQ) mass spectrometer is currently experiencing a renaissance within the proteomics community for its, as yet, unparalleled ability to characterize and quantify a set of proteins reproducibly, completely, and with high sensitivity. Given the immense benefit that high resolution and accurate mass (HR/AM) instruments have brought to the discovery proteomics field, we wondered if highly accurate mass measurement capabilities could be leveraged to provide benefits in the targeted proteomics domain as well. Here, we propose a new targeted proteomics paradigm centered on the use of next generation, quadrupole-equipped HR/AM instruments: parallel reaction monitoring (PRM). In PRM, the third quadrupole of a QqQ is substituted with a HR/AM mass analyzer to permit the parallel detection of all target product ions in one, concerted high resolution mass analysis. We detail the analytical performance of the PRM method, using a quadrupole-equipped bench-top Orbitrap MS, and draw a performance comparison to SRM in terms of run-to-run reproducibility, dynamic range, and measurement accuracy. In addition to requiring minimal upfront method development and facilitating automated data analysis, PRM yielded quantitative data over a wider dynamic range than SRM in the presence of a yeast background matrix due to PRM's high selectivity in the mass-to-charge domain. With achievable linearity over the quantifiable dynamic range found to be statistically equal between the two methods, our investigation suggests that PRM will be a promising new addition to the quantitative proteomics toolbox.