Reliable peak selection for multisample analysis with comprehensive two-dimensional chromatography

Comprehensive two-dimensional chromatography is a powerful technology for analyzing the patterns of constituent compounds in complex samples, but matching chromatographic features for comparative analysis across large sample sets is difficult. Various methods have been described for pairwise peak matching between two chromatograms, but the peaks indicated by these pairwise matches commonly are incomplete or inconsistent across many chromatograms. This paper describes a new, automated method for postprocessing the results of pairwise peak matching to address incomplete and inconsistent peak matches and thereby select chromatographic peaks that reliably correspond across many chromatograms. Reliably corresponding peaks can be used both for directly comparing relative compositions across large numbers of samples and for aligning chromatographic data for comprehensive comparative analyses. To select reliable features for a set of chromatograms, the Consistent Cliques Method (CCM) represents all peaks from all chromatograms and all pairwise peak matches in a graph, finds the maximal cliques, and then combines cliques with shared peaks to extract reliable features. The parameters of CCM are the minimum number of chromatograms with complete pairwise peak matches and the desired number of reliable peaks. A particular threshold for the minimum number of chromatograms with complete pairwise matches ensures that there are no conflicts among the pairwise matches for reliable peaks. Experimental results with samples of complex bio-oils analyzed by comprehensive two-dimensional gas chromatography (GCxGC) coupled with mass spectrometry (GCxGC-MS) indicate that CCM provides a good foundation for comparative analysis of complex chemical mixtures.