Inquiry - Feature Based Molecular Network

[Stephanie Suarez]

Hi all,

I'm new to using the feature based molecular networking (FBMN) portion of the GNPS and I have a couple of question. When I select "View All Library Hits" or "View Unique Library Compounds" after the job is completed, it seems like GNPS only annotated between 3-6 compounds in my samples. When I've done the classical molecular networking, I have this big, beautiful network with around 20-30 annotated by GNPS. I guess the issue that I've come across with FBMN is that I can only select one .mgf file per job, so I've had to run all my samples independently from each other. Does anyone know how I can run a FBMN with all my samples in one job, rather than running them separately? And if I'd like more compounds/hit annotated, should I change some parameters when I process the data in MZMine or would I need to rerun my sample on MS for a longer run time? I appreciate any feedback! Thank you for time as well! 

Thank you,

Stephanie 

[Vanessa Phelan]

Hi Stephanie, 

You can import more than one file into mzmine for processing. I think you may want to revisit the FBMN documentation (there are several super helpful videos embedded as well): https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-mzmine2/ 

Once the dataset (multiple files) is processed through mzmine, there is a specific export function in mzmine formats the ms/ms spectra for molecular networking in gnps through the fbmn workflow. 

If you're still having issues after going through the documentation and videos, please sign up for office hours with Ming: https://ccms-ucsd.github.io/GNPSDocumentation/contact/#gnps-office-hours

Best wishes,

Vanessa