iRT-Pierce combo library import converts all unmodified peptides to K+8, R+10 anatoly.urisman  2020-04-14

Hi Skyline team,
I really like the feature where you can combine multiple blib libraries in Import Peptide Search wizard to create a new combo library. This allows me to use very different search results for iRT peptides (I use Peirce iRT mix, which is K+8 and R+10 modified) and for target peptides (which are usually unmodified) to generate blib files.
However, when I use this combo library to add target peptides, unmodified peptides are incorrectly showing as K+8 and R+10 modified (even though the reference sequences and spectra are correctly showing as unmodified in the library browser). Decoys are also modified as a result. As a work-around I can remove the modifications using Refine --> Advanced --> Remove Label Type (heavy), but I have a feeling that this was not the intended behavior during target import, so just wanted to bring it to your attention.
I've uploaded a file that illustrates this problem (
Thank you for looking into this!

Kaipo responded:  2020-04-27

Hi Anatoly,
This does look like a bug and I agree that the peptides should not have modifications being added to them. Thank you for reporting the issue, I am working on a fix for it.