Hey Brendan,

I've been spending a lot of time using Skyline to perform MS1 analyses and I recently discovered a place for possible future improvement. After importing peptides from a spectral library, I noticed some peptides with ragged ends even though I checked the box to exclude potential ragged ends. Nick looked into this and found that the only features the Spectral Library Explorer takes into account are missed cleavages and precursor charge. I think it would be beneficial if Skyline could also take into account additional peptide and transition filtering options such as the exclusion of ragged ends and peptide length. Otherwise, I find Skyline's ability to perform MS1 analysis very good.

Sincerely,

Scott Goulding