Abstract: A background component of reporter ion signals is determined by fitting a distribution function. A plurality of samples that include a protein labeled with a plurality of isobaric reporter ions is analyzed at a plurality of different times using a mass spectrometer, producing a plurality of mass spectra for the plurality of isobaric reporter ions. A cumulative distribution is calculated for an inverse coefficient of differential expression of the plurality of mass spectra using a processor. A Pearson Type IV distribution shifted by a constant value is fitted to the cumulative distribution and the constant value is solved for using the processor. A background component for each spectrum of the plurality of mass spectra is calculated from the constant value, a calculated coefficient of differential expression for each spectrum, and an average reporter ion signal value for each spectrum using the processor.

Abstract: 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.

Abstract: A background component of reporter ion signals is determined by fitting a distribution function. A plurality of samples that include a protein labeled with a plurality of isobaric reporter ions is analyzed at a plurality of different times using a mass spectrometer, producing a plurality of mass spectra for the plurality of isobaric reporter ions. A cumulative distribution is calculated for an inverse coefficient of differential expression of the plurality of mass spectra using a processor. A Pearson Type IV distribution shifted by a constant value is fitted to the cumulative distribution and the constant value is solved for using the processor. A background component for each spectrum of the plurality of mass spectra is calculated from the constant value, a calculated coefficient of differential expression for each spectrum, and an average reporter ion signal value for each spectrum using the processor.

Abstract: 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.