Fengchao

interact-*.pep.xml files have the probability after rescoring (by PeptideProphet or Percolator), but *.pepXML files don't have it. I have created a ticked to https://skyline.ms/announcements/home/support/thread.view?rowId=57930 Best, Fengchao

FYI, there are some updates in the Skyline forum: https://skyline.ms/announcements/home/support/thread.view?rowId=57930 I think the ideal solution is changing Skyline to make it support MSFragger's new change. If they don't like this...

We have integrated Skyline with FragPipe. People can let FragPipe generate Skyline files seamlessly now. Contact us if you want to try the pre-released versions. Best, Fengchao

Hi Robert, Thanks for your suggestion. We will discuss it internally. Best, Fengchao

I saw similar errors several times before, and it seems to be a Philosopher bug. I always wanted to test or let someone take a look at this bug. Let...

Hi Pete, Thank you very much for your feedback. If I understand it correctly, you want to have a "variable modification group" that variable modification in different groups can't happen...

> For the related but separate issue regarding the large search space, it might be a good approach if different chemical labels could be treated as 2 separate bins ('semi-fixed'...

Hi David, Thanks for your feature request. It is in our waiting list, and we will implement when we have time. But no timeline for it. Best, Fengchao

Same as https://github.com/Nesvilab/FragPipe/issues/923 . We already have a pre-release version that writes apex retention time to psm.tsv file. If you want to test that version, please send an email to...

Hi David, Thanks for your feedback. > However, in the ion.tsv there is still no retention time information. We think of the ion.tsv (when you concatenate all of them) as...