A method of deconvoluting mass spectral data from a complex sample

The present invention provides methods of analyzing mass spectral data based on the 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. One aspect of the invention provides a method of deconvoluting mass spectral data from a complex sample that contains large molecules, such as intact proteins, which are typically ionised to multiple charge states, said method comprising grouping together 3D peaks that have the same retention time and m/z values related according to the following formula:m/z = (M ima)/|i|wherein M represents a proposed neutral mass; mais the molecular weight of a charged moiety; i is an integer; and the +/- relates to whether the charged moiety carries a positive or negative charge.