I am working on phyto-chemical analysis of Cassia angustifolia extracts. GC-MS conditions were used from published literature. I got GC-MS results in the form of graph and a list of 900 compounds. None of the compounds mentioned in the list can be found in literature. Even the most common compounds like kaempferol etc are not present in my extract. What can be the reason for this?
Hi.
You should provide more information. Who did the identification? How did they do it? Which were the GC-MS operating conditions? How are your extracts prepared?
Cheers!
It depends on the column of your appliance and the selection of the condition.
Could you please describe more details about your samples, extraction protocol, derivatization methods, GC column and measurement settings? These are critical informations for GC-MS that could help to answer your question. Best regards.
Dear all, Thank you for your kind responses. I am experimenting with methanolic extracts of C. angustifolia leaves. I used the following conditions for GC-MS procedure:
Initial oven temp: 80C (2 minutes)
Final oven temp: 280C (40 minutes)
total run time: 40 minutes
ionization energy: 1000eV
carrier: Helium
split ratio: 1:5
As mentioned in this article: Article Gas chromatography-mass spectrometry analysis of methanolic ...
what are "derivatization methods" you mentioned in your question? Dr. Thao V. Nguyen
Huda Abbasi Derivatization is a technique used in chemistry which transforms a chemical compound into a product (the reaction's derivate) of similar chemical structure, called a derivative. You need to check if they have the same derivatization method with you (if needed).
You have a list of 900 compounds. You need to obtain some of them in purified form and run them under your conditions, on your equipment as standards for comparison. You have not provided a complete description of what you are doing, but one important parameter to check with the purified compounds would be retention time. Two compounds with similar, but not identical chemical structure may have similar but not identical mass spectra that may be hard to differentiate by simple visual inspection. Without retention time it may be difficult to discern the differences between your compounds. Just a suggestion, you may not want to report results for substances that you can not run standards for. Any machine generated chemical identifications may be inaccurate, so they need to be confirmed with standards.
Dr. Michael Theobald thank you for your response. I'll work on your suggestions.
If you aren't so sure about the Calibration of your machine, try to run same experiments but this time using know verified compounds. Then compare the RTs.
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