A computer-implemented method of analyzing three-dimensional data sets for a plurality of samples, the three-dimensional data sets being obtained from a component separation and mass spectrometer, CS/MS, system, comprising: selecting an ion peak that is present in each of a plurality of two-dimensional data sets obtained from the three-dimensional data sets for each of the plurality of samples obtained from the CS/MS system, wherein the ion peak that is selected is defined as a selected ion peak, each one of the two-dimensional data sets being determined from a respective one of the three-dimensional data sets by selecting a particular point along a first dimension of the three-dimensional data set so that each two-dimensional data set is represented by a second dimension versus a third dimension of the three-dimensional data set at the particular point of the first dimension; determining an area associated with the selected ion peak, using one of a plurality of integration procedures corresponding to a peak origin and a peak terminus, in relation to a baseline intensity, identified for the selected ion peak, for each of the two-dimensional data sets, the area associated with the selected ion peak further corresponding to a relative quantity of a sample component in the respective sample; determining an identity of the sample component associated with the selected ion peak of the two-dimensional data sets; determining the one of the integration procedures used to determine the area of the selected ion peak for a first portion of the two-dimensional data sets, the first portion being defined as the largest number of instances of the two dimensional data sets having the one of the integration procedures applied thereto, the determined one of the integration procedures used to determine the area of the select ion peak for the first portion of the two-dimensional data sets being defined as a template integration procedure; and applying the template integration procedure to the selected ion peaks of a second portion of the two-dimensional data sets, the second portion of the two-dimensional data sets previously having the areas of the selected ion peaks thereof determined by one of the integration procedures other than the template integration procedure, to adjust the relative quantity of the sample component determined to be in the samples corresponding to the second portion of the two-dimensional data sets with respect to the relative quantity of the sample component determined to be in the samples corresponding to the first portion of the two-dimensional data sets. selecting an ion peak that is present in each of a plurality of two-dimensional data sets obtained from the three-dimensional data sets for each of the plurality of samples obtained from the CS/MS system, wherein the ion peak that is selected is defined as a selected ion peak, each one of the two-dimensional data sets being determined from a respective one of the three-dimensional data sets by selecting a particular point along a first dimension of the three-dimensional data set so that each two-dimensional data set is represented by a second dimension versus a third dimension of the three-dimensional data set at the particular point of the first dimension; determining an area associated with the selected ion peak, using one of a plurality of integration procedures corresponding to a peak origin and a peak terminus, in relation to a baseline intensity, identified for the selected ion peak, for each of the two-dimensional data sets, the area associated with the selected ion peak further corresponding to a relative quantity of a sample component in the respective sample; determining an identity of the sample component associated with the selected ion peak of the two-dimensional data sets; determining the one of the integration procedures used to determine the area of the selected ion peak for a first portion of the two-dimensional data sets, the first portion being defined as the largest number of instances of the two dimensional data sets having the one of the integration procedures applied thereto, the determined one of the integration procedures used to determine the area of the select ion peak for the first portion of the two-dimensional data sets being defined as a template integration procedure; and applying the template integration procedure to the selected ion peaks of a second portion of the two-dimensional data sets, the second portion of the two-dimensional data sets previously having the areas of the selected ion peaks thereof determined by one of the integration procedures other than the template integration procedure, to adjust the relative quantity of the sample component determined to be in the samples corresponding to the second portion of the two-dimensional data sets with respect to the relative quantity of the sample component determined to be in the samples corresponding to the first portion of the two-dimensional data sets.