Schematic alignment matrix of partitioned dynamic time warping. Schematic of a pairwise alignment matrix of partitioned dynamic time warping for two arbitrary chromatograms A and B. The light shaded region represents the unconstrained alignment matrix, whereas the dark shaded areas represent the constrained partitions. For every pair of predefined anchors, in this case depicted as mass spectra, a small region around the anchor is kept to allow the alignment a higher degree of flexibility. Each partition is additionally constrained by a local Sakoe-Chiba band constraint. The intersection of all constraint sets defines the final layout of the pairwise alignment matrix and thus the number of elements that are compared and stored.