Table 1.

Peptide sensitivity increases with the use of DeMux and the use of ByOnic's knockout feature, which attempts to make two identifications per spectrum. The numbers shown are the median, minimum, and maximum over the 30 LC runs on rat blood plasma. The percent improvement is relative to ByOnic without the use of DeMux or knockout spectra. Reproducibility of an LC run is defined as the percent of peptides confidently identified in that run that were confidently re-identified in the run's technical replicate.

Type of Search	Proteins Med (Min, Max)	Peptides Med (Min, Max)	Percent Improvement Med (Min, Max)	Peptide Reproducibility Med (Min, Max)
Original DIA Spectra	77 (67, 86)	417 (354, 503)	0.0 (0.0, 0.0)	87.0 (80.8, 90.3)
Original + Knockout	77 (68, 85)	447 (373, 546)	7.0 (3.4, 8.8)	88.5 (82.5, 92.5)
Synthetic Spectra	78 (68, 88)	481 (443, 559)	22.6 (9.3, 27.0)	87.7 (83.9, 91.5)
Synthetic + Knockout	79 (68, 91)	538 (466, 626)	31.5 (21.8, 40.6)	88.0 (82.1, 92.7)