I want to enlist all the characterized secondary metabolites in a certain plant, what database/method I should adopt. So I can say with confidence, for example, that up till now 178 secondary metabolites have been identified from Rosa indica with their molecular weights and chemical formulas.
(This step is crucial for metabolome based phytochemical characterization)
Golm metabolome database run by Joachim Kopka at the Max Planck Institute for Molecular Plant Physiology in Germany provides one of the best online resources. Also associated with Alisdair Fernie.
kind regards
John Moore
Golm metabolome database run by Joachim Kopka at the Max Planck Institute for Molecular Plant Physiology in Germany provides one of the best online resources. Also associated with Alisdair Fernie.
kind regards
John Moore
The Golm metabolome database (Germany), the RIKEN metabolomics group (Japan), the UC Davis group (USA) and the Umea Plant Science centre (Sweden) are amongst the best metabolomics resources research groups to consider; however they naturally work mainly with model organisms and model crops; Arabidopsis, tomato, tobacco, rice and poplar, so for non-model species the study will have to be based on extrapolation or a fair amount of cross-validation using authentic standards.
kind regards
John Moore
Thanks a lot for both answers.
I want to add that these databases are not Species-Metabolite databases, means I want a complete list of metabolites in Parthenium hysterophorus then how can these databases can serve me? I have found one Species-Metabolite database by hit and trial method that is "KNApSAcK: A Comprehensive Species-Metabolite Relationship Database" that give results whatever plant is entered for search. But the problem is that this database is not presenting complete data about a species or presents a limited number of metabolites not the all. Can you please further add something regarding my question?
Dear Huma
I can suggest you contact Halford Dace, a friend of mine who is working on metabolomics.
Alternatively Alisdair Fernie or Joachim Kopka are the real experts and should be able to provide more detailed answers.
kind regards
John
Thanks Ms. Elisabete Carvalho. This is good one but is only representing food components while I'm concerned with plants
Dear Qureshi,
Be aware that only most important species from food, biotech and pharmaceutical importance had been comprehensive studied. All other plants are continuously studying and revisited once a novel technique appears in order to update their metabolomic analysis. At this point you should note its a difficult task to get this kind of info about other species. That is why there are several R&D groups all over the world studying plants metabolomic profile. Besides, plants that are important for some country could not be important for others that's why they did not studied.
Maybe you should do searches in scientific journals to broad the spectra of compounds you already know. But maybe you will find that you are updated and you can´t find more info because there is not more info available for this specie.
This will mean there is a good point to begging to studying it.
Regards,
Gustavo
The Dictionary of Natural Products (Chemnetbase) may prove useful in your specific case. Unfortunately it is pretty pricy...there is a free but only partially complete version which gives some information such as compound names and corresponding molecular formula.
http://dnp.chemnetbase.com/dictionary-search.do?method=view&id=10978606&struct=start&props=&&si=
As the info is not available for all species, I think you should do searches in scientific journals and take notes about the compounds that researchers publish about a specific plant. Some plants are well known and you can find a lot of info including reviews about them, and others just you find little info, because there is not previous
Thanks Dr. Olga Lock....After getting name of metabolite from any publication, can we use databases (PubChem, ChemSpider, HMDB etc.) as authentic source for further information like molecular weight, chemical formula and structure etc.?
Dear Huma
Now that you have added an answer to another question on similar lines, you can check other databases detailed in that thread for more detailed answers to your query.
Good luck.
Check this thread for databases:
https://www.researchgate.net/post/How_can_one_collect_the_complete_information_of_a_plants_phytochemicals
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