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

[Chambers, M. <mat...@gm...>]

Hi Gerd,

The vendor peak picking algorithm refers to the raw data's vendor, not the output format. If those are Thermo .raw files, then it's Thermo's 
peak picking. Mascot Distiller does its own peak picking on the raw data, and naturally that peak picking is optimized to work with Mascot. 
If you search with a different engine (MS-GF+, X! Tandem, MyriMatch, Morpheus, etc.), I bet you'll find that Thermo's peak picking is 
usually better.

The different number of entries is a little surprising though. Can you identify the extra/missing entries? See if those are alternate charge 
states of spectra already included at a different charge state.

Hope this helps,
-Matt


On 3/28/2019 7:20 AM, Gerd wrote:
> 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
>
>
>
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