Hello,

I am writing to ask whether there is a plug-in or other option that enables more reliable automated peak picking in Skyline for large datasets.

In our workflows, Skyline frequently selects the highest-intensity peak, which is often incorrect. Even when I manually select the correct peak and apply it to all subsequent the alignment remains inaccurate for a substantial number of cases. This is particularly challenging in degradation assays, where we need Skyline to prioritize peak selection at the expected retention time—even when the signal is weak or largely background. At present, this does not appear to be feasible with the available settings.

If there are recommended approaches, plug-ins, or configuration strategies that would improve automated peak selection and retention time adherence at scale, I would greatly appreciate your guidance. Reviewing hundreds of samples across multiple peptides individually is highly time-consuming, and a more robust one-click solution would significantly improve efficiency.

Thank you for your assistance.