Although parameters, such as mass tolerance and intensity threshold (which define the real peak versus noise), can be regarded as relatively instrument-dependent (or a property of acquired data), they can be changed (within certain limits): mass tolerance can be set to the mass accuracy of the acquired data (which was 4.9 mDa in this study) and twice this value; hence, in this study mass tolerance was varied within these limits (0.005 and 0.01 Da). Considering the complexity and high-dimensionality of the samples (particularly in plant metabolomics), and considering the mathematical limitations of chemometric algorithms, it is essential to explore the processing methods (combinations of sets of parameters: selected as objectively and optimally as possible) so as to maximize the mining of the raw data.