Skyline for crosslinked peptides MSe Waters data analysis

Skyline for crosslinked peptides MSe Waters data analysis floriana capuano28104  2023-01-05 06:44


I have found a previous post suggesting that Apex3D pepxml files can be uploaded in Skyline. I am planning to use skyline to identify two crosslinked peptides and I would like to use the output of UNIFI data search to build an ion library and gain confidence in peak picking. I understand from previous posts that it is possible to use PLGS csv output, however at this stage I would not know how to add additional modifications in PLGS. I can see that UNIFI allows to export results in mzml and mgf format. Is there any chance I could directly use these to built the ion library? UNIFI is doing a targeted analysis to match spectra to peptides from one or two proteins added to the processing method. Would this have an impact on dotp or confidence in peak picking? Many thanks, Floriana

Nick Shulman responded:  2023-01-05 07:36
This page has the list of all of the types of peptide search results that Skyline understands:
I do not see anything about "Unifi" in that list, but maybe you will see a format in that list which you have.

By the way, Skyline understands crosslinked peptides. You can see some information about how to use the crosslinked peptide features in Skyline here:

There are several peptide search engines which know how to look for crosslinked peptides. If you were using the crosslinked peptides feature in Skyline, you would usually want to use search results from one of the crosslink-aware peptide search engines. The types of crosslinked peptide search results that can be used with Skyline now are Byonic, pLink, and MeroX. In order to use these crosslinked peptide search results in Skyline you would first need to convert the search results to a format called ".proxl". I can point you to where you can get download a proxl converter if you want to use a particular
crosslinked peptide search engine.

I am not sure I understood your question but I hope this helped.
-- Nick