Fig. 2: Low FPR and reliable feature matching in DIA-ME.

A False positive rate, i.e. percentage of detected E.coli peptides, in non-spiked 1-ng H.sapiens samples (N = 7) for different types of data analysis and DIA software. Analyses without spiked samples, i.e. without entrapped matching, are indicated in green and grey (light-: without MBR, dark-: MBR), while co-analyses with spiked samples are indicated in blue and brown for DIA-NN and Spectronaut, respectively. The shade of the color indicates the E.coli spiking ratio. Error bars are shown as mean ± sd. B Receiver operating characteristics (ROC) of default q-value filters in DIA-NN (left) and Spectronaut (right) for data analyses involving spiked ME samples with 10% spiking ratio (DIA-NN: light blue (1:1) to dark grey (100× DIA-ME), Spectronaut: light brown (1:1) to black (100× DIA-ME)). Areas under ROC (AUROC) are indicated in parentheses, while the diagonal line represents a random classification. C False transfer rate, i.e. percentage of E.coli peptides among identifications that were transferred by matching, in non-spiked 1-ng H.sapiens samples (N = 7) for different types of data analysis and DIA software. Rate was set to 100% when fewer H.sapiens peptides but more E.coli peptides were identified after matching. Color-coding as in (A). Error bars are shown as mean ± sd. Source data are provided as a Source Data file.