biostudies-literatureSherwood CANHLBI NIH HHSNCI NIH HHSNIGMS NIH HHS3746-51https://www.ebi.ac.uk/biostudies/studies/S-EPMC2811718biostudies-literatureUnknown8(7)Multiple reaction monitoring (MRM) is a highly sensitive method of targeted mass spectrometry (MS) that can be used to selectively detect and quantify peptides based on the screening of specified precursor peptide-to-fragment ion transitions. MRM-MS sensitivity depends critically on the tuning of instrument parameters, such as collision energy and cone voltage, for the generation of maximal product ion signal. Although generalized equations and values exist for such instrument parameters, there is no clear indication that optimal signal can be reliably produced for all types of MRM transitions using such an algorithmic approach. To address this issue, we have devised a workflow functional on both Waters Quattro Premier and ABI 4000 QTRAP triple quadrupole instruments that allows rapid deteJournal of proteome researchRapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets.PMC2811718R21 CA126216-02N01-HV-28179R21 CA126216P50GM076547P50 GM0765475R21CA126216N01HV28179P50 GM076547-03Eastham ALee LWFalkner JASherwood CAMirzaei HMartin DBRisler JfalseRapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets.Multiple reaction monitoring (MRM) is a highly sensitive method of targeted mass spectrometry (MS) that can be used to selectively detect and quantify peptides based on the screening of specified precursor peptide-to-fragment ion transitions. MRM-MS sensitivity depends critically on the tuning of instrument parameters, such as collision energy and cone voltage, for the generation of maximal product ion signal. Although generalized equations and values exist for such instrument parameters, there is no clear indication that optimal signal can be reliably produced for all types of MRM transitions using such an algorithmic approach. To address this issue, we have devised a workflow functional on both Waters Quattro Premier and ABI 4000 QTRAP triple quadrupole instruments that allows rapid dete2009-01-01T00:00:00Z2009 Jul2025-04-05T11:31:45.301Z2019-03-27T00:28:09ZS-EPMC28117181940552210.1021/pr801122b