In our preprint, 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 xx of the preprint. Eessentially, GoldenHaystack was able to quantify accurately nearly all peptides in the MS, whether identified or not.