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No matching mod for PTM when using MaxQuant

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No matching mod for PTM when using MaxQuant jonas elsborg  2025-03-13 09:59
 

Dear Skyline team,
I am trying to analyze my msms.txt output file from MaxQuant.
I did a DDA experiment, where localize several PTMs which I defined myself. Specifically, I am looking at ADP-ribosylation.

I imported the mqpar.xml and the modifcations.xml as requested, but i get the following error:

"Skyline (64-bit) 24.1.0.414 (5b5ea5889c)

System.IO.IOException: ERROR: No matching mod for ad in sequence AE(ad)PVEVVAPRGK (line 861). Make sure you have provided the correct modifications[.local].xml file."

My ADP-ribosylated peptides are reported as (ad) by MaxQuant, but it seems that this is incompatible with Skyline. It is not clear to me how Skyline interprets the modifications.xml file, since the shorthand notation found for several PTMs is not found in that file. Similarly, it is also not clear to me if i would be able to define these PTMs myself elsewhere in Skyline to circumvent the modifciations.xml import.

So far i tried to rename modifications, subset the file, use different MQ versions, but all to no avail. If there is a work-around that would allow be to analyze my results in Skyline then that would be great. Thanks a lot for a great piece of software,
Best,
Jonas
 
 
jonas elsborg responded:  2025-03-13 10:07

The msms.txt was too large, i attach an exempt here with some problematic rows.
Thanks.
 
Nick Shulman responded:  2025-03-13 12:49
The modification that BiblioSpec is trying to find is:
ADP-ribosylation (CDEHKRSTY)

That modification name does not exist in the "modifications.xml" file that you provided.
There are similar names such as "Ubi-ADP-ribosylation (CDEHKRSTY)" or "ADP-ribosylation (DEKRS)" but BiblioSpec needs to find the one with the exact name match.
Do you maybe have a different modifications.xml file which does contain "ADP-ribosylation (CDEHKRSTY)"?

By the way, if you ever want to send us files which are larger than the 50MB attachment size limit on these support requests you can upload those big files here:
https://skyline.ms/files.url
-- Nick
 
jonas elsborg responded:  2025-03-13 15:49
Hi again,
Thank you so much for your reply. It seems that my modifications.xml indeed got mixed up during all the manual hacking of the file I was attempting. So you exactly were able to pinpoint my problem! Thanks!
I was able to import most modifications, but since ADPr is a complex PTM that targets many different amino acids, it seems some were lost/not interpreted correctly.
I assume it is fine if I manually configure this under settings>peptide settings>modifications>edit list>add ?

Does Skyline "update" automatically, or do I need to reimport when I make changes?

Just for my curiosity, how does Skyline know that _peptid(ad)e_ in the msms.txt corresponds to ADP-ribosylation? In the modifications.xml and mqpar.xml I cannot find "(ad)" anywhere, which makes me suspect that you use a database for this (unimod?) that is not accessible to me. Since not all modifications are defined in unimod, it could make sense that I would have to manually define this afterwards.

Thank you for your help, this is really valuable for me. Great tip about large attachments too!
/Jonas
 
Nick Shulman responded:  2025-03-13 16:04
In the msms.txt file there are multiple columns. One column ("Modifications") has the names of the modifications like "ADP-ribosylation (CDEHKRSTY)". A different column "Modified sequence" has the sequence with the modification abbreviations "AE(ad)PVEVVAPRGK".
BiblioSpec has some complicated code to figure out which modification abbreviation in the "Modifications" column for that row corresponds to which thing in the "Modified sequence".
You can see the C++ code for that here:
https://github.com/ProteoWizard/pwiz/blob/581e01ffc3bacd0df73d2a75693ad5a0ac844d02/pwiz_tools/BiblioSpec/src/MaxQuantReader.cpp#L963

Modifications in .blib files are only described by their mass. If the modification can be found in the list of Unimod modifications, Skyline is usually pretty good at guessing which modification that mass is supposed to be.
When you are defining your own modifications in Skyline you can use whatever name you want so long as it has the same mass as what is in the .blib file.

The following webinar is very helpful for learning about working with modifications in Skyline:
https://skyline.ms/Webinar10.url
-- Nick
 
jonas elsborg responded:  2025-03-18 04:50
Hi Nick,

I just wanted to say thank you for your help, this was really great advice. I also enjoyed the webinar.
Thank you for explaining the principle behind parsing the msms.txt too, that was helpful.
Best,
/Jonas