Can Skyline generate iRT assay library file used in Mobi-DIK script? Z. Jiang  2021-02-24

Dear Skyline team,

I am recently trying to use Mobi-DIK to analyze diaPASEF data. I was wondering if there is any way using Skyline to create the iRT assay library file that is used in the script "python --pasefdata data.d --mqout path/to/maxquant_data --irt irt_file.tsv"?


Brendan MacLean responded:  2021-02-24

Maybe better directed at the Roest lab? Skyline definitely gets used to produce assay libraries for OpenSWATH. Though, I am not sure where the documentation for this lives.