Hi Skyline Team,

I'm new to using Skyline, and I've went through some of the available tutorials to start me off.

I want to create a spectral library using dia-PASEF data, so I can do a peptide search of the data.

I've been able to upload my data using: File > Search > Run Peptide. I've managed to upload my .d folders and select my settings under the DIA workflow. My trouble is at the Conversion settings (where DIA-Umpire creates the pseudo-DDA files for searching), the preset instruments available do not have an option for the timsTOF.

How do I go about continuing with building the spectral library? Would you suggest that I should rather use dda-PASEF data for spectral library building and search my dia-PASEF data against that instead?

Thank you for your time.

From: Rethabile