Dear Skyline team,
thanks for developing skyline and your consistent support. I use Skyline (version 220.127.116.1169, 64-bit) for analyzing a DIA data set of 15 .raw files (Thermo) by a library of 300 raw files (both samples and library ran with iRT's). The settings I used are pretty much the same as they are recommended in the two DIA-Webinars. For my analysis, I have adjusted the iRT and used shuffled decoys implemented in skyline, then I tried to improve the peak scoring by using mProphet.
However, in the outcome not all options are available (see the figure attached) that may can lead to an improvement of the peak scoring.
And secondly, I experienced while exporting protein list following group comparison that the proteinlists varies a lot between different treatments (from 10.500 down to 500). Is there any default filtering criteria (hidden) which reduces the number of exported protein lists within one analysis file?
Thank you for your comments and suggestions. I would be happy to help you out if this is necessary!