[proteowizard-support] Problem with peakPicking filter and resulting .mgf files

[Gerd <ger...@mp...>]

Dear msconvert community and developers,

I am an undergrad from MPI for biophysical chemistry in Göttingen, 
Germany who is just starting out with his thesis so please forgive me if 
my question was already answered somewhere else.

I want to convert a large number of .raw files automatically to .mgf 
format using the msconvert command line tool on Win10. These .mgf files 
should be comparable to .mgf files created with Mascot Distiller that we 
routinely use in our work.

Therefore, I am using the --filter "peakPicking vendor msLevels=1-" 
argument to utilize Mascot DLLs for peak picking.

The problem is that .mgf files converted with this option still yield 
.mgf files of different size compared to the .mgf file generated from 
the same .raw file with Distiller. Moreover, database search of those 
two files revealed that the number of MS/MS scans corresponding to 
entries in the database was lower in .mgf file generated with msconvert 
compared to the one generated with Mascot Distiller as well as lower 
protein scores. The number of entries identified in the mgf files 
obtained with msconvert was also lower - 388 vs 398 obtained with 
Distiller.

Are there any additional options in msconvert that I am forgetting to 
include that might help me with this problem? Or is there any way to use 
default .opt files with processing options supplied with Mascot 
Distiller to configure msconvert conversions?

Best regards,

Gerd