Rapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets

Carly A. Sherwood, Ashley Eastham, Lik Wee Lee, Jenni Risler, Hamid Mirzaei, Jayson A. Falkner, Daniel B. Martin

Research output: Contribution to journalArticlepeer-review

55 Scopus citations


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 peptideto-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 determination of the optimal value of any programmable instrument parameter for each MRM transition. Here, we demonstrate the strategy for the optimizations of collision energy and cone voltage, but the method could be applied to other instrument parameters, such as declustering potential, as well. The workflow makes use of the incremental adjustment of the precursor and product m/z values at the hundredth decimal place to create a series of MRM targets at different collision energies that can be cycled through in rapid succession within a single run, avoiding any run-to-run variability in execution or comparison. Results are easily visualized and quantified using the MRM software package Mr. M to determine the optimal instrument parameters for each transition.

Original languageEnglish (US)
Pages (from-to)3746-3751
Number of pages6
JournalJournal of Proteome Research
Issue number7
StatePublished - Jul 6 2009


  • Collision energy
  • Cone voltage
  • Multiple reaction monitoring (MRM)
  • Optimization
  • Selective reaction monitoring (SRM)
  • Targeted proteomics
  • Triple quadrupole

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)


Dive into the research topics of 'Rapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets'. Together they form a unique fingerprint.

Cite this