.mgf file (ms/ms) file filtering

[Mustafa B.]

Hi,

I wanted to ask if there is a way to filter out redundant ms2 inputs from a.mgf file. I have run several samples (approx. 600) in ddms2 and during the extraction of ms2 (combined into 1 .mgf file), i get redundant ms2 inputs, which overcrowds my molecular networking output. Therefore, I wanted to ask if there is a quick way of filtering those.

Cheers,

Mustafa  

[Mingxun Wang]

You could run classical molecular networking with clustering turned on (which is default). 

Ming

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[Mustafa B.]

Hi Ming,

thanks for the quick reply, I just run the classical molecular networking (settings are on the 1. picture below), and I still get the redundancy in my molecular network (see 2. picture below).

I basically extracted from all my .raw files the ddMS2 data using RefinerMS, resulting in an approx. 1.9 GB .mgf file. I guess the problem is because of the different RTs that those parent ions are associated to (2.picture). 

Do you know any method that can cluster the ddMS2 spectras based on an RT window into few? 

Or is there a way in GNPS to overlook the RTs? 

Would it be possible to delete the RT row in the .mgf file (or is it required for the MolNet), perform MolNet? - would the result then eliminate the redundancy....

Thanks a lot.

Mustafa