Odd NEM error when builidng library from MaxQuant results (but not Mascot)

support
Odd NEM error when builidng library from MaxQuant results (but not Mascot) Jason Held  2019-08-11
 

I've built (not quite literally, but close) a million skyline libraries with IAC and NEM modified cysteines from Mascot and MaxQuant searches. I haven't changed anything and my IAC modified cysteines are importing fine, but I'm getting the attached error when I try to import a MaxQuant MSMS.text file. A .dat file from mascot imports both IAC and NEM modified peptides just fine. Both NEM mods in Skyline and Maxquant are the same (H7C6NO2), supported by the happy imports from Mascot.... This is a MaxQuant-specific problem. I'm not sure why I'm getting the error and suddenly unable to build a library from the MaxQuant MSMS.txt file.

I've attached screenshot of the error and the msms.txt file.

Cheers,
Jason

 
 
matt.chambers42 responded:  2019-08-12

Hi Jason,

I don't see the attachment. Is the problem with output from the 1.6.7 version?

 
Jason Held responded:  2019-08-13

That attachment was too big apparently. FTP?

I'm using MQ 1.6.6.0. IAC modified peptides went in fine, just not the NEM ones.

Cheers,
Jason

 
Brendan MacLean responded:  2019-08-13

Hi Jason,
You should be able to post to:

https://skyline.ms/files.url

Thanks for your help in reproducing this issue.

--Brendan

 
matt.chambers42 responded:  2019-08-13

Hmm, a screenshot should not exceed the attachment size threshold. Try again? If it's still too big, try saving as PNG.

I know the 1.6.5 vs 1.6.7 uses a different way of inserting the mod into the sequence in msms.txt, but I'm not sure about 1.6.6. 1.6.7's output will be fixed soon but is broken in the current daily. Are your IAC vs. NEM modifications set up differently, i.e. one variable and one fixed?

 
Jason Held responded:  2019-08-13

sorry the msms.txt file was too big to attach. screenshot attached.

both mods are variable in the search and in skyline (its a cys redox preotomics dataset).

Again, IAC mods seem to be fine, its just NEM.

 
Jason Held responded:  2019-08-13

I tried to uploaded the msms.txt file to the FTP but I get the attached error.

 
Brendan MacLean responded:  2019-08-13

This may be a problem we have seen with overwriting and existing file. You don't have permission to overwrite something someone else has uploaded, and there may already be a file there named msms.txt (its a pretty generic name). Try renaming your msms.txt to something more specific like jason_held_msms.txt

That will likely work. Thanks for your effort.

--Brendan

 
matt.chambers42 responded:  2019-08-13

The Skyline/BiblioSpec error you got indicates your modifications.xml file doesn't contain the mentioned modification. Did you customize the modifications.txt file (possibly in the GUI)? If so you'll need to put the customized modifications.xml file next to the msms.txt.

 
Jason Held responded:  2019-08-13

Yes, moving the modifications.xml file to the same directory as the msms.txt file worked. No idea why that suddenly need to happen in order to import, but its solved. Thanks- Jason