Patent ID: 7919745

Claim:
A method for calculating a corrected reporter ion intensity in tandem mass spectrometry based quantitation using isobaric labels, comprising: labeling an analyte in each of two or more samples of a mixture of samples with a different isobaric label resulting in the use of two or more isobaric labels; eluting the analyte from the mixture of samples using a separation technique and measuring intensities of the eluting analyte using a mass analysis technique; selecting an analyte intensity at each of at least two times from the measured intensities of the eluting analyte producing at least two analyte intensities; performing tandem mass spectrometry on the eluting analyte at each of the at least two times producing a plurality of reporter ion intensities that represent each permutation of the two or more isobaric labels and the at least two times; creating a system of linear equations expressing each reporter ion intensity of the plurality of reporter ion intensities as a sum of a background noise intensity and a product of a fragmentation efficiency and one of the at least two analyte intensities; and calculating a corrected reporter ion intensity from a solution of the system of linear equations.