In our paper, we ran a dilution series experiment (11 dilution points, 5 technical replicates per point; Thermo Astral dataset; single pooled plasma sample) to assess the degree to which GoldenHaystack could accurately quantify peptides. The details are in section IV of the paper. Essentially, GoldenHaystack was able to quantify accurately nearly all peptides in the MS, whether identified or not.