Fig. 3.

Example retention time parameter estimation in a set containing four features sharing identifications (“A,” “B,” “C,” “D”) between a file pair. The correct match known beforehand is marked with a corresponding letter in the top table. Features without identity are denoted N/A. The time difference for all possible matches, based on the set m/z tolerance and charge between the four features from the first file and all features detected in the second file, are shown in the panel to the right (eight in total). For feature “B,” the match with the smallest time difference is not the feature with corresponding identity. Precision and recall is computed in the bottom panel for four different retention time tolerances. They are equivalent to the list of the smallest retention time differences for each feature, as these represent the minimum cost in terms of FPs for including a TP. Both identity- and occurrence-based metrics are computed as seen in the table. Abbreviations used in the table: Tol, Tolerance; Prec, Precision; Occ, Occurrence-based; Id, Identity-based. When two settings result in the same sum of precision and recall, the setting that results in the highest recall is selected. Here, the retention time tolerance used for subsequent alignment would be set to 5 min.