Simultaneous discovery of compounds dominated by either molding kinetics or geographical region of origin for moisture damaged cacao beans using orthogonally applied tile-based fisher ratio analysis of GC×GC-TOFMS data.

Herein, two "orthogonal" characteristics of moisture damaged cacao beans (temporally dependent molding kinetics versus the time-independent geographical region of origin) are simultaneously analyzed in a comprehensive two-dimensional (2D) gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS) dataset using tile-based Fisher ratio (F-ratio) analysis. Cacao beans from six geographical regions were analyzed once a day for six days following the initiation of moisture damage to trigger the molding process. Thus, there are two "extremes" to the experimental sample class design: six time points for the molding kinetics versus the six geographical regions of origin, resulting in a 6 × 6 element signal array referred to as a composite chemical fingerprint (CCF) for each analyte. Usually, this study would involve initial generation of two separate hit lists using F-ratio analysis, one hit list from inputting the data with the six time point classes, then another hit list from inputting the dataset from the perspective of geographic region of origin. However, analysis of two separate hit lists with the intent to distill them down to one hit list is extremely time-consuming and fraught with shortcomings due to the challenges associated with attempting to match analytes across two hit lists. To address this challenge, tile-based F-ratio analysis is "orthogonally applied" to each analyte CCF to simultaneously determine two F-ratios at the chromatographic 2D location (F-ratio and F-ratio) for each hit, by ranking a single hit list using the higher of the two F-ratios resulting in the discovery of 591 analytes. Further, using a pseudo-null distribution approach, at the 99.9% threshold over 400 analytes were deemed suitable for PCA classification. Using a more stringent 99.999% threshold, over 100 analytes were explored more deeply using PARAFAC to provide a purified mass spectrum.