Crosslink search from Mascot to create library for Skyline

Crosslink search from Mascot to create library for Skyline sandberg  2020-08-05

Is it possible to use crosslinking results from the Mascot search engine to create a library to search the files for crosslinked peptides in Skyline?


Brendan MacLean responded:  2020-08-05

Hi Magdalena,
You are the first to request it. So far we have only built support for Proxl XML ( for crosslink search results. Proxl has a set of converters from raw search results to Proxl XML. You can find a list of the existing converters at the bottom of this page with links to their GitHub projects:

I do not see one for Mascot.

However, we would like to begin adapting our existing native search results readers to support results with crosslinked peptides. If you can provide us with an example for Mascot, we can look into adapting the Skyline (BiblioSpec) Mascot library builder to support it. We can also point the developer responsible for Proxl converters to your example data, and he likely will be interested in creating a converter for it.

Thanks for posting to the Skyline support board. We look forward to working with you to extend our support for crosslinking experiments.


sandberg responded:  2020-08-06

Hi Brendan,

Thank you very much for your response! I have uploaded the data from a search in Mascot for disulfide bridges in a GM-CSF sample digested with GluC + Chymotrypsin into the file sharing folder. The file is called"GM-CSF disulfide bridges". It would be great if you could use this data to adapt the Mascot library builder to support crosslink results. It would also be great if you could send it to the Proxl converters to possible make a converter for Mascot files.

Please let me know if you need any additional data or have any questions.

Best wishes,