| Nick Shulman responded: |
2022-01-18 08:12 |
What problems are you running into with Bromide modifications? Skyline is supposed to be able to handle those just fine.
Skyline used to have a problem where Skyline could not modifications involving these less common elements in MaxQuant search results. We fixed that bug back in Novemeber, so if you're using the latest Skyline 21.2, MaxQuant search results with Bromine should work.
What type of peptide search results do you have and what sort of problems are you running into?
If you would like to send us some files to take a look at you can upload them here:
https://skyline.ms/files.url
-- Nick |
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| bianca dempsey responded: |
2022-01-18 11:02 |
Hi, Nick!
Thanks for answering! We are trying to build a library from MaxQuant DDA search with BrTyr and Br2Tyr modifications in several proteins. I attached the error we are having related to the modifications. What could we do?
Thank you! |
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| Nick Shulman responded: |
2022-01-18 11:15 |
If you install Skyline-Daily, you will be able to use MaxQuant search results that use these exotic elements.
I was mistaken about this bug having been fixed in Skyline 21.2. The fix actually only made it into Skyline-Daily.
You can install Skyline-Daily from here:
https://skyline.ms/project/home/software/Skyline/daily/begin.view?
-- Nick |
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| bianca dempsey responded: |
2022-01-19 04:05 |
Hello, Nick!
Thank you for your reply! I'm having the same issue (attached) when trying to build the library. Do you think it could be something related to the MaxQuant configurations? I haven't had this problem when I used a normal DDA acquisition, without bromide modifications.
Thank you! |
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| Nick Shulman responded: |
2022-01-19 04:21 |
Can you send me your MaxQuant search results? It sounds like something else must be going wrong besides the thing that we fixed in Skyline-Daily.
It sounds like we will need your files "msms.txt", "mqpar.xml" and "modifications.xml" and probably your spectrum file too (.mzML, or whatever file you searched with MaxQuant).
You can upload those files here:
httsp://skyline.ms/files.url
-- Nick |
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| bianca dempsey responded: |
2022-01-19 11:15 |
Hi, Nick!
I've just uploaded the DDA files in a .zip folder "DDA BrTyr".
We have extracelular matriz samples from mouse with possible modifications of Br addition in Tyr residues. In the MaxQuant search we added BrTyr and Asn -> Asp as variable modifications, besides Met oxidation.
Thank you for your help! |
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| Nick Shulman responded: |
2022-01-19 11:50 |
Thank you for uploading that file.
Do you have a file called "modifications.xml" (or maybe "modifications.local.xml")?
I believe BiblioSpec looks for a file of that name and expects to be able to find the definitions of modifications in there. You probably have a file with one of those names somewhere near your peptide search results, and if you copy that file into the same folder as "msms.txt" it will probably work.
If it does not work, then please send me your modifications.xml file.
Files which are less than 50MB can be attached to this support request. You can upload larger files here:
https://skyline.ms/files.url
-- Nick |
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