Although we have observed up to ~2000% more quantified peptides by quantifying dark proteome, it matters little whether this increase is ~20%, ~200%, ~2000%, or ~20,000%.

Instead, the key argument is this: the peptides constituting the dark proteome are biologically valuable, yet they are no more / no less likely to be seen by the MS than those generic FASTA sequences (i.e., the MS is unbiased). So, if there is reasonable chance that those biologically valuable but unexpected sequences or PTMs exist in your DIA-MS data files, we at GoldenHaystack Lab can (a) quantify them and then (b) analyze all the quantified peptides — whether present in the known protein libraries or in the dark proteome — through a sophisticated AI/ML routine that creates a small (typically << 200), parsimonious peptide panel that maximally separates study conditions (e.g., please see HUPO 2025 poster ).

Finally, for any desired follow-up work, such as targeted MS validation or manual/semi-automated denovo sequencing, we can provide all the required information (e.g., peptide's elution times and MS1/2 m/z values etc.) and help you in any other useful ways to make the follow-up work almost trivially easy to do.