• Sign In
  1. Requests

Apex biotin-phenol modification spectral library

support

View Request

view list print
Apex biotin-phenol modification spectral library daniswan  2018-05-11 17:15
 

I have done some APEX proximity labeling experiments in which I enrich for Y-biotin phenol sites using anti biotin. I would now like to build a spectral library to perform targeted quantification of these sites. I have searched the data with MaxQuant and tried importing the peptide search as usually done, but it is not recognizing the Y-biotin phenol modified peptides in my msms.txt file and these are being excluded from the spectral library. I have added the Y-biotin phenol modification to the list of modification in the peptides settings. Is there some text from the msms.txt and skyline settings that needs to match in a certain way for these peptides to be imported properly?

Thanks!

-Danielle
 
 
Brendan MacLean responded:  2018-05-11 18:00
Hi Danielle,
The Skyline library builder gets its modification information for MaxQuant runs from the mqpar.xml file. Make sure it is defined in there and that Skyline can find it. It can be inany of 3 directories: sames msms.txt, parent and grandparent.

Hope that helps. Thanks for using Skyline.

—Brendan
 
daniswan responded:  2018-05-12 09:09
In the mqpar.xml file there is a section that has the following information:

 <variableModifications>
      <string>Oxidation (M)</string>
      <string>Acetyl (Protein N-term)</string>
      <string>Biotin Phenol (Y)</string>
 </variableModifications>

Then in the msms.txt file the sites of biotin phenol are designated by xxxxY(bi)xxxxx in the peptide sequence. I do not see anywhere in the mqpar.xml file where skyline would get the exact mass for the modification, does it also look in another file for the mass? or that mass matching is from my peptide modifications within skyline?

Thanks!

-Danielle
 
Kaipo Tamura responded:  2018-05-12 12:44
Hi Danielle,

The modification mass is calculated from information in the modifications.xml file (from its composition). You can check what the library builder calculated its mass as through the Spectral Library Explorer in Skyline, or using a SQLite browser application like SQLite Expert.

Thanks,
Kaipo
 
daniswan responded:  2018-05-12 19:58
I have figured it out. I think MaxQuant might have changed some files. Now user added modifications are found in modifications.local.xml

Here is how I got to work:
1. copy the modifications.local.xml and modifications.xml to the same directory as msms.txt
2. append the Biotin Phenol modification information from modifications.local.xml to the end of the modifications.xml file
3. The Biotin Phenol on Y modification was added as a structural modification option in my peptide settings (I had done this already, just noting for reference)

Best,

-Danielle
 
Matt Chambers responded:  2018-06-25 10:59
Hi Danielle,

Sorry for the delay and thanks for the report. I will soon look into automatically picking up the .local.xml file as well as the original.

Thanks,
-Matt