Abstract: A method for analyzing spectra comprises identifying a set of sample peaks in a sample spectrum, where the sample peaks are associated with fragments of a sample, each having a sample fragment mass. A reference spectrum is selected with one or more reference peaks corresponding to fragments of a reference, each having a reference fragment mass. A mass difference can be determined between selected sample and reference peaks, and a group exchange can be selected based on the mass difference; e.g., where the group exchange represents a change in the sample or reference fragment masses associated with the selected peaks. The selected peaks can be shifted by the mass difference, and a fit value can be determined with respect to the reference spectrum. The fit value characterizes similarity between the respective sets of sample and reference peaks, responsive to the group exchange and corresponding peak shift.