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Topic: How to predict MS/MS spectrum of a given chemical that is not present in Pubchem (Read 220 times) previous topic - next topic

How to predict MS/MS spectrum of a given chemical that is not present in Pubchem

Dear all,
Does anybody know how to predict MS/MS spectrum of a given chemical that is not present in Pubchem by MS-FINDER?  I am working with oligomers which could be any combination of monomers, e.g. diethylene glycol (DEG), phthalic acid (PA), triethylene glycol (TEG). However,  many of them are not present in Pubchem, for example, cyclic TPA-EG-TPA-DEG. I am thinking if MS-FINDER can work like a MS/MS fragmentator that allows input of a given structure and give us the in-silico MS/MS spectrum?


Thanks in advance!
Sukis.



Re: How to predict MS/MS spectrum of a given chemical that is not present in Pubchem

Reply #1
hi Sukis,

in such case you need to create custom database (tab separated .txt file) with compounds of your interest containing
Title   InChIKey   Short InChIKey   PubChem CID   Exact mass   Formula   SMILES   Comment

example file attached.
As far as I remember formula and smiles are the crucial fields.

Best, romas



Re: How to predict MS/MS spectrum of a given chemical that is not present in Pubchem

Reply #2
Hi Rromanas Chaleckis,

Thanks a lot. I know that we can prepare a .txt file as you said. But as I understand, in this case, MS-FINDER will fragment all chemicals provided in the .txt file and score them according to their matches to the given spectrum. However, I am thinking if it is possible to fragment a given chemical requiring no given spectrum.

Re: How to predict MS/MS spectrum of a given chemical that is not present in Pubchem

Reply #3
Hi Sukis,

the only program for your purpose should be CFM-ID. It can generate the predicted spectrum from a given structure.
Although it's not the function for predicting fragments, MS-FINDER has an option (in commandline) to generate all of possible fragments from a given structure by like:

MsfinderConsoleApp.exe generate -i .\msfinder-generator\lysoPE.smiles -o .\msfinder-annotator\lysoPEs-result.txt

Thanks,

Hiroshi
 

Re: How to predict MS/MS spectrum of a given chemical that is not present in Pubchem

Reply #4
Many thanks, Hiroshi. I will give it a try.