Fig. 4: Three representative peptides that were quantifiable below 1 ng.

a Each row displays a peptide chromatogram at each dilution within the 1 ng curve. Each peptide contains three representative transitions. The first peptide from Granzyme B had the best estimated LoQ at 0.043:1, while the third peptide from IL-2 receptor subunit alpha had an estimated LoQ at 0.132:1 at 1 ng. b LoQ and LoD were estimated on a peptide-by-peptide basis using EncyclopeDIA’s curve fitting algorithm. First, the algorithm determines a maximum line through the noise of the calibration curve and then fits the linear dynamic range. The intersection of both lines is the LoD (shown with a gray shaded, empty circle), while the LoQ (shown at the intersection of the dotted red lines) is three standard deviations of the noise above the LoD. The error associated with the lines fitted through the noise and linear, dynamic range are shown in yellow, and represent 3 standard deviations above and below the median signal for each line.