isobarQuant with the Maxquant search engine

[Ekaterina Vansovich]

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 

Ekaterina 

P.S. Sorry for the long question.