Quantification of mixture components from their composite optical or mass spectra is a common need in analytical chemistry. We encountered the need when applying a combination of enzymatic digestion with nuclease P1 and tandem mass spectrometry to a mixture of isomeric photomodified oligodeoxynucleotides. In the procedure, we collisionally activated the [M - H]- or [M + Na - 2H]- ion of trinucleotide triphosphates, which were extricated enzymatically from the larger, damaged oligodeoxynucleotides, and we measured the relative abundances of characteristic fragment ions. The results sometimes yield curved calibrations for plots of the relative fragment ion abundances in the product ion spectra of isomers versus their relative amounts. We developed a normalized linear model, which brings understanding to the nonlinear plots and allows quantification of the mixture components from their composite spectra. The outcome demonstrates a general quantification procedure and shows that different yields for generating fragment ions from different constituents of the mixture cause the curved calibration lines.