A system for detecting a product ion of a modified form of a known compound of interest in a sample from tandem mass spectrometry data, comprising: a processor that (a) receives a plurality of sample product ion spectra produced by separating known compounds from a sample over time using a separation device, and at each time step, analyzing the known compounds by performing a plurality of product ion scans for a plurality of precursor mass selection windows selected across a mass range of the sample using a tandem mass spectrometer, (b) retrieves known mass-to-charge ratio (m/z) values of product ions of at least one compound of the known compounds from a memory, (c) generates product ion extracted ion chromatograms (XICs) from product ion spectra of the plurality of sample product ion spectra that include m/z peaks matching the known m/z values, (d) groups XIC peaks of the generated product ion XICs by retention time, producing a plurality of XIC peak groups, (e) selects at least one XIC peak group of the plurality of XIC peak groups, (f) creates an m/z peak list for the at least one XIC peak group by obtaining the m/z value for each monoisotopic peak in each spectrum used to generate the XIC peaks of the at least one XIC peak group, (g) removes from the m/z peak list m/z values that match the known m/z values, (h) for each m/z value remaining in the m/z peak list, calculates an m/z difference between the peak list m/z value and each m/z value of the m/z values of the known product ions, producing a plurality of m/z difference values, (i) groups m/z difference values of the plurality of m/z difference values with same m/z value into groups and counts the number of m/z difference values in each group, producing a plurality of m/z difference value groups that each includes a count, and (j) if a count of an m/z difference value group of the plurality of m/z difference value groups exceeds a predetermined count, detects a product ion of a modified form of the at least one compound at the m/z value of the m/z difference value group. (a) receives a plurality of sample product ion spectra produced by separating known compounds from a sample over time using a separation device, and at each time step, analyzing the known compounds by performing a plurality of product ion scans for a plurality of precursor mass selection windows selected across a mass range of the sample using a tandem mass spectrometer, (b) retrieves known mass-to-charge ratio (m/z) values of product ions of at least one compound of the known compounds from a memory, (c) generates product ion extracted ion chromatograms (XICs) from product ion spectra of the plurality of sample product ion spectra that include m/z peaks matching the known m/z values, (d) groups XIC peaks of the generated product ion XICs by retention time, producing a plurality of XIC peak groups, (e) selects at least one XIC peak group of the plurality of XIC peak groups, (f) creates an m/z peak list for the at least one XIC peak group by obtaining the m/z value for each monoisotopic peak in each spectrum used to generate the XIC peaks of the at least one XIC peak group, (g) removes from the m/z peak list m/z values that match the known m/z values, (h) for each m/z value remaining in the m/z peak list, calculates an m/z difference between the peak list m/z value and each m/z value of the m/z values of the known product ions, producing a plurality of m/z difference values, (i) groups m/z difference values of the plurality of m/z difference values with same m/z value into groups and counts the number of m/z difference values in each group, producing a plurality of m/z difference value groups that each includes a count, and (j) if a count of an m/z difference value group of the plurality of m/z difference value groups exceeds a predetermined count, detects a product ion of a modified form of the at least one compound at the m/z value of the m/z difference value group.