MALDI spectra not creating nodes

[Allyson McAtamney]

Hi everyone,

I am working in GNPS2 in the classical molecular networking workflow, and my input data contains 14 MALDI-MS/MS spectra, all with different precursor masses. However, I am only getting 6 nodes in my molecular network. I tried disabling clustering, and that resulted in 5 nodes. It seems like I am "losing" spectra somewhere, as they aren't appearing in my network at all. Additionally, I have reduced my networking filters to a cosine score of 0.5 and 2 matched peaks for the minimum. Everything else I have left as the default settings. 

Can anyone tell me why I am not getting the same number of nodes as I have input spectra? Additionally, how can I possibly fix this?

Thank you,

Allyson McAtamney

5th year PhD Candidate

Sanchez Lab

UC Santa Cruz