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?
P.S. Sorry for the long question.