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

Wanted to import .msp spectral libraries from:

.msp import works for HMDB, MoNA and ReSpect but NOT for GNPS, Fiehn HILIC and LipidBlast (throws an error message, see example attached) from

Spectral library import from
does not work at all, i.e. shows zero molecules after import


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.