We are trying to set up an automated pipeline for High Throughput Proteomics. As a first step, we're going to use Skyline Runner to automate the communications. Predictably, I've already run into a few issues (admittedly, I'm not the most expert Skyline User).
My plan was to set up a specific method as a Settings file. So questions:
1. Can I specify a spectral library in a settings file?
2. I'd like to export an isolation list with Skyline's prediction of the best 3 peptides and best 3 fragments for each protein. I managed to limit to the top 3 fragments. How do I limit number of peptides per protein.
Thanks
Alex

Please post to the support board. This is not really the right venue for your questions.