The details of how LOD is calculated in QuaSAR are described in the on-line version of Addona, et al, 2009, Nat. Biotechnology. The online experimental methods should contain the details - I will post them once I can get my hands on them.
The other reference is Abbatiello, et al, 2015, MCP (see attachment). I'm pasting the description in the experimental section below (reference 5 is the Addona 2009 Nat Biotech paper, reference 42 is Currie, L. A. (1968) Limits for qualitative detection and quantitative determination. Application to radiochemistry. Analytical chemistry 40, 586-593):
Determination of LOD and LOQ: Limit of detection for all monitored peptides from the 9-
point response curve in 0.5 μg/μL depleted plasma were determined as previously
described (5, 42). Once the LOD was determined separately for each peptide transition,
the LOQ was calculated using the customary relation: LOQ = 3 x LOD (43). The LOD
was based on the variance of the blank sample (sample A, digested depleted plasma
with the heavy isotope peptides and no analyte spiked in) and the variance of the lowest
level spike-in sample (sample B, with analyte at 1 amol/μL). Assuming a type I error rate
α=0.05 for deciding that the analyte is present when it is not, and a type II error rate
β=0.05 for not detecting the analyte when it is present, the LOD was derived as:
LOD = LOB + cβ x SDS
LOB (limit of blank) was defined as the 95th percentile of the blank A1 samples (44).
This was estimated as the mean plus t1-β x SDb, where SDb was the standard deviation in
the blank samples, and SDS was the standard deviation of the low-level spike in sample
B. For a relatively small number of repeated measurements for sample B, cβ was
approximated as t1-β where t1-β is the (1-β) percentile of the standard t distribution on f
degrees of freedom, where f is the number of replicates minus 1. Detailed calculations
of the various components of the LOD are listed in the QuaSAR LOD/LOQ output tables
for each site, which are available on the Panorama webserver for the manuscript.
LOD values are initially calculated for all three transitions monitored for each peptide.
The transition with the minimum LOD is chosen as the “best” transition. This transition is
used to report LOD and LOQ for inter- and intra-lab CV calculations.