Ultrafast and Robust Optimization of Peptide MRMs Using a Fast-Scanning Triple Quadrupole Mass Spectrometer

Targeted proteomics methods may be composed of tens or hundreds of MRM channels corresponding to peptides from a wide variety of proteins of interest. Although precursor and product ions can be calculated in advance, the best ions for monitoring among all possible channels need to be selected and confirmed before analyzing a large or material-limited sample set. Similarly, collision energy and other instrument parameters may be estimated or modeled by software but require fine-tuning and verification to maximize instrument response for each channel. A fast-scanning triple quadrupole mass spectrometer has been used with proteomics software to verify and optimize large numbers of MRM transitions with a minimum number of optimization runs.