The present invention provides, inter alia, methods of analyzing mass spectral data based on charge states of analyte ions. In some embodiments, the methods can be used for differential profiling of samples, such as comparing a sample comprising a given compound and a sample comprising metabolites of the same compound. The methods can also be used to identify and isolate biomarkers. Systems for performing the methods, as well as computer-readable media for performing the methods, are also described.