MSP Spectral Library import for small molecules failed stolltho  2020-05-17
 
Hi there.

Wanted to import .msp spectral libraries from:
https://mona.fiehnlab.ucdavis.edu/downloads
https://minedatabase.mcs.anl.gov/#/download
http://prime.psc.riken.jp/compms/msdial/main.html#MSP

.msp import works for HMDB, MoNA and ReSpect but NOT for GNPS, Fiehn HILIC and LipidBlast (throws an error message, see example attached) from https://mona.fiehnlab.ucdavis.edu/downloads

Spectral library import from
https://minedatabase.mcs.anl.gov/#/download
http://prime.psc.riken.jp/compms/msdial/main.html#MSP
does not work at all, i.e. shows zero molecules after import

win10
skyline-daily 20.1.1.134

cheers,
Thomas
 
 
Brian Pratt responded:  2020-05-18
Hi Thomas,

Thanks for the report. I had already found the MoNa/LipidBlast problem with the formula being strangely formatted when the precursor_type is "[M+]", that should be fixed in the next Skyline-Daily.

MSP is a very loose "standard" in the way that FASTA is a "standard", everybody seems to find a different way to express things within the confines of the format. There is still work to do on the MoNA/LipidBlast import to pick out all the useful information (SMILES, InChiKey etc) that's crammed into the "Comments" field, but what I have ready to go does get the name and strangely formatted formula in so that's a good step forward.

I will investigate the others as well. Please do not hesitate to alert us to any other problems you find.

Thanks for using the Skyline support board!

Brian Pratt
 
stolltho responded:  2020-05-18
Thanks Brian for your swift reply.
I actually don't need the libraries at the moment.
Just wanted to let you guys know, since others might encounter the same issue.
Cheers,
Thomas