search

CCMS-UCSD / GNPS_Workflows

Public Workflows at GNPS
https://gnps.ucsd.edu/
Other
52 stars 43 forks source link

Adding LipidBlast to the proposed libraries #87

Open lfnothias opened 5 years ago

lfnothias commented 5 years ago

I have been testing the LipidBast library in the static folder on the NIST serum sample. https://www.nature.com/articles/nmeth.2551 https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=0d89db67b0974939a91cb7d5bfe87072 As you can see, it works extremely well for lipid annotation and so it would nice to make it available to users. However I would not recommend to make it selected by default, as it is pretty big (200k+) and it requires a minimum match peaks of 2-3.

mwang87 commented 5 years ago

Do you know if these libraries are real spectra are in silico?

justinjjvanderhooft commented 5 years ago

https://fiehnlab.ucdavis.edu/projects/LipidBlast

These are in-silico spectra - hence the scale....

mwang87 commented 5 years ago

Cool, I have a proposed solution, we can start moving GNPS libraries to the CCMS_SpectralLibraries location, and what we'll do is start with LIPIDBLAST. Maybe we'll make prebuilt link to select it, it'll be like:

  1. Standard Molecular Networking
  2. Molecular Networking for LIPIDBLAST
lfnothias commented 5 years ago

That's a great idea as it will make sure it is used the right parameters. Yeah it is in silico, but for lipids the prediction is simple.