Varying the mass tolerance parameter (which specifies the mass accuracy of the acquired data) and intensity threshold parameter (which specifies the threshold of a spectral peak) resulted in different data matrices from the same LC-MS raw data, and the different numbers of variables (in the multivariate X-space) and noise levels are tabulated in Table 1. Theoretically, an infinite number of combinations for sets of processing parameters with MarkerLynxTM are possible. In practice, the computational time to process one combination of a set of parameters could be in hours, depending on the size of the datasets. Furthermore, understanding of the underlying algorithms and steps involved in the data processing is essential so as to decide which parameter to vary. As indicated in the experimental section, parameters, such as mass tolerance and the intensity threshold (which define the real peak versus background noise), can be changed, within certain limits: for instance 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 in these limits (0.005 and 0.01 Da). The mass tolerance (mass accuracy) parameter is the basis by which the ApexTrack algorithm determines the regions of interest in the m/z domain, whereas the intensity threshold parameter is used in the peak removal step, defining the resultant noise level and redundancy in the data matrix. These two parameters are essential, hence this study explored the impact of these on the creation of the data matrix.