A corrected reporter ion intensity is calculated in tandem mass spectrometry based quantitation using isobaric labels. An analyte in each of two or more samples of a mixture of samples is labeled with a different isobaric label. The analyte is eluted from the mixture of samples and intensities of the eluting analyte are measured. An analyte intensity is selected at each of at least two times from the measured intensities. Tandem mass spectrometry is performed on the eluting analyte at each of the at least two times. A plurality of reporter ion intensities is produced. A system of linear equations is created expressing each reporter ion intensity of the plurality of reporter ion intensities as a sum of a background noise intensity and the product of a fragmentation efficiency and an analyte intensity. A corrected reporter ion intensity is calculated from a solution of the system of linear equations.