panoramaProteomicsLilian HeilHomo Sapienshttps://panoramaweb.org/qLITvsqOT.urllheil2@uw.eduUniversity of WashingtonPanoramaPublicParallel reaction monitoring (PRM) is an increasingly popular alternative to selected reaction monitoring (SRM) for targeted proteomics. PRM's 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.Comparison of Unit Resolution Versus High-Resolution Accurate Mass for Parallel Reaction Monitoring.Heil Lilian R LR, Remes Philip M PM, MacCoss Michael J MJreaction.reaction.liquid chromatography tandem mass spectroscopy, Fresh, FBgn0003149, CG1849, ion, Fresh Frozen Plasma, determination, SRML1, Peptidomics, Blood, leg, number, FBN, Gene, presence, LC-MS-MS, l(1)AA33, Polypeptides, Para, peptido, TOF, mPM, ECTOL1, sensitive, LC-MSMS, Gene Products, 1, 2, CG5939, sensitivity, WMS, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, LCMSMS, MRM, peptides, iones, Runt, chemical analysis., ions, free, OCTD, allergic reaction, reaction, l(1)B2/13.1, RUN, Run, scientific observation, Blood Plasmas, Sensitivity, peptidos, GPHYSD2, plasma, SPS1, LB5, SGS, LC-MS2, measuring, l(1)LB9, Frozen Plasma, DmelCG5939, PAPT, Proteins, DmelCG1849, LC-MS/MS, Rnt, SPDSY, Plasmas, Peptide, AA33, Multiple Reaction Monitoring, ACMICD, lLB5, Frozen Plasmas, count in organism, LC/MS/MS, Ionen, prm, chemical analysis, Protein, l(3)S010605, MFS1, WMS2, Plasma, 0106/05, PM/mPM, Specificity, portion of plasma, l(1)19Ea, MASS, Protein Gene Products, P235, Gene Proteins, l(3)10631, Ion, Specificity and Sensitivity, liquid chromatography-tandem mass spectroscopy, SSKS, liquid chromatography tandem mass spectrometry, Peptid, assay, Polypeptide, pm, PMliquid chromatography tandem mass spectroscopy, Fresh, FBgn0003149, CG1849, ion, Fresh Frozen Plasma, determination, SRML1, Peptidomics, Effects, Blood, leg, number, FBN, Gene, presence, Long Term, LC-MS-MS, l(1)AA33, Polypeptides, Para, peptido, mPM, ECTOL1, sensitive, LC-MSMS, Gene Products, 1, 2, CG5939, Effect, sensitivity, WMS, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, LCMSMS, MRM, peptides, Longterm, iones, Runt, chemical analysis., Long-Term, ions, free, OCTD, allergic reaction, reaction, l(1)B2/13.1, RUN, Run, scientific observation, Blood Plasmas, Sensitivity, peptidos, Long-Term Effect, GPHYSD2, Long-Term Effects, plasma, SPS1, LB5, SGS, LC-MS2, measuring, l(1)LB9, Frozen Plasma, DmelCG5939, PAPT, Proteins, DmelCG1849, LC-MS/MS, Longterm Effect, Rnt, SPDSY, Plasmas, Peptide, AA33, Multiple Reaction Monitoring, ACMICD, lLB5, Frozen Plasmas, count in organism, LC/MS/MS, Ionen, prm, Long Term Effects, chemical analysis, Protein, l(3)S010605, MFS1, WMS2, Plasma, 0106/05, PM/mPM, Specificity, portion of plasma, l(1)19Ea, MASS, Longterm Effects, Protein Gene Products, P235, Gene Proteins, l(3)10631, Ion, Specificity and Sensitivity, liquid chromatography-tandem mass spectroscopy, SSKS, liquid chromatography tandem mass spectrometry, Peptid, assay, Polypeptide, pm, PMfalseComparison of unit resolution versus high-resolution accurate mass for parallel reaction monitoringParallel reaction monitoring (PRM) is an increasingly popular alternative to selected reaction monitoring (SRM) for targeted proteomics. PRM’s 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 a 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 on over 62% of peptides in the assay.Thu Aug 19 00:00:00 GMT+01:00 2021PXD023334960634319745