The MarkerLynxTM application uses the patented ApexTrack (termed also ApexPeakTrack) algorithm to perform accurate peak detection and alignment. MarkerLynxTM initially determines the regions of interest in the m/z domain based on mass accuracy (mass tolerance). The ApexTrack algorithm controls peak detection by peak width (peak width at 5% height) and baseline threshold (peak-to-peak baseline ratio) parameters. In this study, these parameters were calculated automatically by MarkerLynxTM. The ApexTrack also calculates the baseline noise level using the slope of inflection points. Thus, for peak detection, the ApexTrack algorithm consists of taking the second derivative of a chromatogram and locates the inflection points, the local minima, and peak apex for each peak, to decide the peak area and height. A “corrected” Rt is then assigned and the data are correctly aligned, with the alignment of peaks across samples within the range of user-defined mass and Rt windows. Following the peak detection, the associated ions are analyzed (the maximum intensity, its Rt and exact m/z mass) and captured for all samples.