isobarQuant with the Maxquant search engine

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Ekaterina Vansovich

Oct 5, 2021, 1:44:22 PM10/5/21
to Andromeda Help
Hi everyone, 

I'm new at working with MS data and I hope maybe someone more experienced could help me here :) 
I'm trying to use the isobarQuant package with the Maxquant search engine for TPP experiments. isobarQuant output files are in mgf format, so I`ve been trying to convert mgf files to mzXML format for Maxquant as it follows:

 mgf ---> mzXML
OpenMS FileConverter with the  force_MaxQuant_compatibility parameter. 
The files I get after this step don't work with MaxQuant, probably because of 64-bit encoding. 
That's why I use MSConverter:
mzXML from FileConverter ----> mzXML 32-bit encoding. 
After these two steps, MaxQuant does the search without giving any error. But it doesn't find anything.
Trying to find out what a problem it can be I've compared the converted mzXML file with the original mgf file and it looks like the converted file has the following errors: 
retentionTime is always "PT1S" among all scans,
activationMethod=CID versus HCD in the original mgf file 
the number of scans in the converted file is less than in the original. 
the scan number doesn't correspond to a peptide how it is in the original file. 
There is a way to avoid the above errors occurring during conversion? 
Or maybe there is a better way to use isobarQuant with the Maxquant search engine than converting mgf to mzXML? 

Best regards 

P.S. Sorry for the long question. 
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