Journal
JOURNAL OF PROTEOME RESEARCH
Volume 20, Issue 9, Pages 4435-4442Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.1c00377
Keywords
parallel reaction monitoring; targeted proteomics; plasma
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Funding
- National Institutes of Health [P41 GM103533, U01 DK121289, U19 AG065156]
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PRM is a popular alternative to SRM for targeted proteomics, monitoring all product ions in a single spectrum. High-resolution data is not necessary to obtain high-quality quantitative data. Both mass analyzers, Orbitrap and linear ion trap, show similar technical precision but the linear ion trap has superior sensitivity and lower limits of quantitation for over 62% of peptides.
Parallel reaction monitoring (PRM) is an increasingly popular alternative to selected reaction monitoring (SRM) for targeted proteomics. PRMs strengths over SRM are that it monitors all product ions in a single spectrum, thus eliminating the need to select interference-free product ions prior to data acquisition, and that it is most frequently performed on high-resolution instruments, such as quadrupole-orbitrap and quadrupole-time-of-flight instruments. Here, we show that the primary advantage of PRM is the ability to monitor all transitions in parallel and that high-resolution data are not necessary to obtain high-quality quantitative data. We run the same scheduled PRM assay, measuring 432 peptides from 126 plasma proteins, multiple times on an Orbitrap Eclipse Tribrid mass spectrometer, alternating separate liquid chromatography-tandem mass spectrometry runs between the high-resolution Orbitrap and the unit resolution linear ion trap for PRM. We find that both mass analyzers have similar technical precision and that the linear ion trap's superior sensitivity gives it better lower limits of quantitation for over 62% of peptides in the assay.
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