Flow injection electrospray mass spectrometry (FIE-MS) metabolite fingerprinting is widely used as a 'first pass' screen for compositional differences, where discrimination between samples can be achieved without any preconceptions. Powerful data analysis algorithms can be used to select and rank FIE-MS fingerprint variables highly explanatory of the biological problem under investigation. We describe how to create a species-specific FIE-MS/MSn metabolite database and how to then query the database to predict the identity of highly significant variables within FIE-MS fingerprints. The protocol details how to interpret m/z signals within the explanatory variable list based on a correlation analysis in conjunction with an investigation of mathematical relationships regarding (de)protonated molecular ions, salt adducts, neutral losses and dimeric associations routinely observed in FIE-MS fingerprints. Although designed for use by biologists/analytical chemists, collaboration with data-mining experts is generally advised. The protocol is applicable in any areas of bioscience research involving FIE-MS fingerprinting.