The GC-MS of a horse urine extract obtained 40 h after doping with quinine is analysed. An unresolved cluster of peaks is studied. Several problems occur specifically with GC-MS data, which are solved using chemometrics methods. The use of windows to select masses, with the diagnostic masses changing according to window size and position, is discussed and used in calculations of derivatives to determine the composition of the chromatogram. PCA loadings and scores plots are obtained. The use of deconvolution to obtain clean spectra of the metabolites together with pseudo-simulations for determination of underlying peak-shapes is described.