1. A mass spectrometry method for identifying differences in the level of one or more analytes between two or more sample sets comprising the steps of: (a) obtaining spectra for individual samples of said two or more sample sets, wherein said spectra comprise m/z-intensity pairs, wherein an m/z intensity pair comprises an m/z identifier and a signal associated with said m/z identifier, (b) for each said m/z identifier of one or more m/z identifiers from said m/z intensity pairs, determining a relationship between the corresponding signals in said spectra, and (c) assigning each said relationship a rank or value based on both within-sample-set and between-sample-set signal distributions, wherein said rank or value is a measure of a likelihood that said signal arises from an analyte having a different level between said two or more sample sets.