Fig. 2: FDR filtering and library coverage.

a Peak groups detected and quantified by DIAMetAlyzer in a APM spiked-in human blood plasma dilution series (SWATH - 30 samples) filtered by different FDR thresholds. Without FDR filtering (no FDR), we detected and quantified the highest number of true positive peak groups (TP; n = 3479), but also the highest number of false positive peak groups (FP; n = 1471). At 5% FDR, 3071 true peak groups and 125 false positives were quantified (3.9%). At 1 % FDR the true positive peak groups were further reduced (n = 2523), so were the false positives (n = 19; 0.7%). b Individual pesticide mixes in solvent (around 30 pesticides each) were used to construct the target-decoy assay library. Stringent filtering allows high-quality assays to be used in library construction: Around 9% of the pesticides could not be detected in the data. An additional 14% were not identified via MS1 or did not possess a valid MS2 spectrum (4+ peaks, to allow for fragment annotation). 77% of the pesticides were automatically detected, identified, and annotated. In the library construction step, filtering by the number of transitions greatly affects the coverage of metabolites (three transitions: 60% coverage, two transitions: 71% coverage, one transition: 77% coverage).