Multiple-Reaction-Monitoring (MRM) is a method to quantify peptides based on peak signal intensities in MS/MS spectra. In short, the abundance of a peptide is estimated by summing the intensities of selected fragment ions in its MS/MS spectra.
The advantages of this method are high sensitivity and accuracy of quantitation. It stems from drug testing and research, but it is increasingly applied in proteomics. For details, see Anderson and Hunter (2005) "Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins" Molecular and Cellular Proteomics 5.4 pp. 573-588.
Obviously, we need to know the precursor masses and charges of the peptide ions we want to monitor as well as the m/z values of the fragment ion used for quantitation. These values are usually determined in a first LC-MS run of the sample using targeted MS/MS.
The input to this program consists of a list of precursor m/zs and fragment ion m/zs. It performs a quantitation as explained above and writes a list of peptide features with the estimate abundance.
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