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,

sandberg responded:  2020-09-25

Hi Brendan,

Would it be possible to build the library containing crosslinking results if I got the data into an .ssl file?


matt.chambers42 responded:  2020-09-25

Hi Magdalena,

We're discussing how to support crosslinking in SSL now, but it's currently not supported. The Mascot support we will also add but it's not a simple fix. How do you plan to get your results into SSL?


sandberg responded:  2020-09-28

Hi Matt,

Ok, that is great to hear. Disulfide search results in Mascot can currently be converted into a csv file that can be imported by a web-based tool for cross-linking analysis called xiView and they are working on a converter to the ssl file format. I also just thought that the ssl file format looked kind of simple so that it might be possbile to make a converter from csv file to ssl directly. However, the csv file only contains disulfide linked peptides so if one wanted to have a library containing all identified peptides some workaround would be needed.


Brendan MacLean responded:  2020-09-28

Curious how Matrix Science is expecting to write SSL files. Do they have a spec for what those files would look like?

Our currently supported SSL format is detailed here:

As Matt notes, we are going to try to extend it to support crosslinked peptides, but we aren't aware of an existing spec for how to achieve this.

sandberg responded:  2020-10-09

It is actually the guy responsible for maintaining the xiView software, Colin Combe, who has promised a converter from imported crosslinking data into xiView to the .ssl format. I don't know how he imagines the spec should look but he says that they already have a converter internally at their uni.

This is the contact webpage for the xiView crew:

matt.chambers42 responded:  2020-10-09

I've responded to the GitHub issue for their SSL export: