I am trying to identify secondary metabolites from plant active over cancer cell lines. I am new to metabolomics. So from where should I start?
If you want to try to identify the secondary metabolites , first you need to check the type of compounds already isolated from the plant. Can be from same species or genus. Then from the type of compounds, for example eburnane type alkaloids or dammarane triterpenes. Usually each particular type of compounds will have typical fragmentation peaks and major peaks. From the profile of mass fragmentation , one may identify the metabolites in the extracts. however, to be sure of the identity of certain metabolite, one still has to isolate and run Nmr as isomers may be difficult to differentiate in mixtures/ extract.
All the best.
Dear Awang,
Thanks for the answer but what about plant where no such study done so for. Another thing I am focusing LC-MS based metabolomics.
Dear Saurabh,
Look at other plants from same genus. usually they have similar compounds and some of the compounds may even be same. But if you find no particular patern of a certain type of compound, then you may have to isolate and purify and follow the normal procedure of characterisation.
One important thing to note is that a peak ,especially a prominent one, may not represent one compound. If mixtures then the ms fragmentation that you see may be misleading . So please be careful. Sometimes the peaks that you are interested in are obscured ok.
All the best, I believe you can do it
To isolate the secondary metabolite extensive review especially from website like http://www.ars-grin.gov/duke/ should be done, it can give you idea about the plant you are interested in, any further improvement in method of isolation can than be considered, have a essential resources for metobolomics, decide the process suitable etc.
I used to do that ten-fifteen years ago. Scale up chromatography, purify compound of interest up to 95%. HRMS, NMR should give an answer. Alternatively find a lab having LC-MS-NMR coupling and run you sample. One can have online ms, ms/ms and H1-NMR data sufficient for structural assignment.
Yes, I agree , if you can get the service of LCNMRMS , this will surely simplify the process and in Australia I believe you can get the service. However, be cautious - do not easily jump to conclusions, as you are dealing with complex mixtures. Get assistance from natural products chemist and spectroscopist for your analysis.
All the best
Hi,
to start with read:
Plant Metabolomics
Methods and Protocols
Editors: Nigel W. Hardy, Robert D. Hall
ISBN: 978-1-61779-593-0 (Print) 978-1-61779-594-7 (Online)
Some resources:
http://prime.psc.riken.jp/
http://www.massbank.jp/?lang=en (read the manuals!)
https://xcmsonline.scripps.edu/
Be carefull about the experimental setup and the appronbiate(negative) controls.
Hope this helps.
Cheers,
Holger
- Badges
- Science topic