theoretical fragments

Topic: theoretical fragments (Read 9128 times) previous topic - next topic

theoretical fragments

February 28, 2012, 02:15:42 AM

Hi,
I have been using your METLIN database for performing metabolite identification. Its been very useful for us. I am in the process of writing an algorithm for an in-house tool. I am wondering how the theoretical fragments are generated? Are there any set of rules I can refer, similar to Domon-Costello nomenclature for glycans and Murphys table for Glycerophospho lipids etc?

I will appreciate for any sort of help.

Thanks in advance.

Re: theoretical fragments

Reply #1 – February 28, 2012, 11:45:15 AM

It calculates possible fragment structures using an in silicio fragmentation approach (Wolf et. al.)
and then matches these theoretical fragments to the observed fragments, considering some modifications and different ion types.

Re: theoretical fragments

Reply #2 – February 29, 2012, 01:25:07 AM

Hi Ralf
Thanks for your prompt reply. I have gone through the publication "In silico fragmentation for computer assisted identification of metabolite mass spectra" referred by you and believe they are employing band disconnection approach. Can this approach be used for all classes of metabolites for generating the in-silico fragments for MS/MS fragment match?

Can you please refer me any further papers where I can find detail information about in-silico fragmentation of metabolites, like flow steps are described, though approach might differ?

Thanks in advance.

Re: theoretical fragments

Reply #3 – February 29, 2012, 01:14:14 PM

The only other papers I'm aware of are Heinonen et. al. and Hill et. al., also referenced in the Wolf et. al. publication.