A system for scoring peaks of a known compound of interest from a collection of mass spectra, comprising: a separation device configured to separate one or more compounds from a sample mixture; a mass spectrometer configured to perform at each time interval of a plurality of time intervals one or more mass spectrometry scans on the separating sample mixture using one or more sequential mass window widths in order to span an entire mass range producing: a mass spectrum for each sequential mass window width, one or more mass spectra for the entire mass range for each time interval of the plurality of time intervals, and a collection of mass spectra for the plurality of time intervals; and a processor configured to (a) select a fragment ion of a known compound, (b) calculate an extracted ion chromatogram for the fragment ion from the collection of mass spectra, wherein the XIC includes an intensity of the fragment ion for each interval of the plurality of time intervals, and (c) if two or more XIC peaks corresponding to the fragment ion are found in the XIC at two or more different time intervals, analyze a mass spectrum of the entire mass range from the collection of mass spectra for each of the two or more different time intervals by comparing values of one or more ion characteristics of a mass-to-charge ratio (m/z) peak of the fragment ion in each entire mass range mass spectrum of the two or more entire mass range mass spectra to one or more known values for the fragment ion, and base the score of each XIC peak of the two or more XIC peaks of the fragment ion on the results of the comparison. a separation device configured to separate one or more compounds from a sample mixture; a mass spectrometer configured to perform at each time interval of a plurality of time intervals one or more mass spectrometry scans on the separating sample mixture using one or more sequential mass window widths in order to span an entire mass range producing: a mass spectrum for each sequential mass window width, one or more mass spectra for the entire mass range for each time interval of the plurality of time intervals, and a collection of mass spectra for the plurality of time intervals; and a mass spectrum for each sequential mass window width, one or more mass spectra for the entire mass range for each time interval of the plurality of time intervals, and a collection of mass spectra for the plurality of time intervals; and a processor configured to (a) select a fragment ion of a known compound, (b) calculate an extracted ion chromatogram for the fragment ion from the collection of mass spectra, wherein the XIC includes an intensity of the fragment ion for each interval of the plurality of time intervals, and (c) if two or more XIC peaks corresponding to the fragment ion are found in the XIC at two or more different time intervals, analyze a mass spectrum of the entire mass range from the collection of mass spectra for each of the two or more different time intervals by comparing values of one or more ion characteristics of a mass-to-charge ratio (m/z) peak of the fragment ion in each entire mass range mass spectrum of the two or more entire mass range mass spectra to one or more known values for the fragment ion, and base the score of each XIC peak of the two or more XIC peaks of the fragment ion on the results of the comparison. (a) select a fragment ion of a known compound, (b) calculate an extracted ion chromatogram for the fragment ion from the collection of mass spectra, wherein the XIC includes an intensity of the fragment ion for each interval of the plurality of time intervals, and (c) if two or more XIC peaks corresponding to the fragment ion are found in the XIC at two or more different time intervals, analyze a mass spectrum of the entire mass range from the collection of mass spectra for each of the two or more different time intervals by comparing values of one or more ion characteristics of a mass-to-charge ratio (m/z) peak of the fragment ion in each entire mass range mass spectrum of the two or more entire mass range mass spectra to one or more known values for the fragment ion, and base the score of each XIC peak of the two or more XIC peaks of the fragment ion on the results of the comparison.