I have performed GC-MS analysis of Phytochemicals from a medicinal plants and also identified compound using NIST library. After NIST identification, I have a list of compounds. I am constructing a phytoconstituent table for manuscript which include compound name, retention time, area percentage, molecular formula and nature of compounds. I am trying to identify the class/nature of phytochemicals (like flavonoids, carotenoids, phenols or polyphenols, glycosides, tannins etc). For that, I am searching each compounds on databases like PlantaeDB, IMPPAT 2.0, website like MedChemExpress and also literature search. Some compounds can be find here but many of the are not to be found anywhere.
1. How to identify the class of phytochemicals or secondary metabolites after GC_MS and NIST identification?
2. Some compounds are repeated with different retention time and Similarity index. Which one to include and on what basis?
3. In one extract, more than 60 compounds are identified. Should I include them all for manuscript or can I select the important and bioactive compounds only?
Very much thankful for your help!
Identifying the class of phytochemicals and determining which compounds to include in your manuscript after GC-MS and NIST identification involves a systematic approach. Here are the steps to address your queries:
1. Identifying the Class of Phytochemicals
To identify the class of phytochemicals or secondary metabolites, you can follow these steps:
a. Database Searches:
- PlantaeDB and IMPPAT are good starting points. Ensure you are using the correct chemical names and synonyms.
- PubChem and ChemSpider can also be useful for finding information about the chemical structure and its known classes.
b. Literature Search:
- Use databases like Google Scholar, PubMed, and ScienceDirect to search for scientific articles related to the identified compounds. Keywords like "phytochemical class" or "secondary metabolite class" along with the compound name can help.
c. Chemical Structure Analysis:
- Analyze the chemical structure using software tools like ChemDraw or MarvinSketch to predict the class based on known structural features of flavonoids, carotenoids, phenols, etc.
d. Expert Consultation:
- If certain compounds are hard to classify, consider consulting with a phytochemist or a researcher specializing in natural products chemistry.
2. Handling Repeated Compounds
When you have repeated compounds with different retention times and similarity indices, consider the following:
a. Consistency Check:
- Check the consistency of identification across different runs. If the same compound is identified consistently with a high similarity index, it is likely accurate.
b. Retention Time Comparison:
- Retention time differences can sometimes indicate different isomers or derivatives. Compare the retention times and the similarity indices to choose the most reliable identification.
c. Reporting:
- If the similarity index is significantly different, consider reporting both and discussing the possible reasons (isomerism, different sources of the compound within the plant, etc.).
3. Selection of Compounds for the Manuscript
Including all identified compounds versus selecting important ones depends on the focus of your manuscript:
a. Relevance and Impact:
- Include compounds that are known to have significant biological or pharmacological activity relevant to your study.
b. Novelty:
- Highlight compounds that are newly identified or have unique properties not commonly reported.
c. Focused Analysis:
- For a more focused analysis, you can prioritize compounds based on their relative abundance (area percentage), biological significance, and the objectives of your study.
d. Supplementary Data:
- Consider including the complete list of compounds in supplementary materials while discussing the key bioactive compounds in the main text.
Practical Steps:
1. Data Organization:
- Create a comprehensive table of all identified compounds with their retention times, area percentages, molecular formulas, and similarity indices.
2. Class Identification:
- Use a combination of database searches, literature reviews, and chemical structure analysis to classify each compound.
3. Selection Criteria:
- Define clear criteria for selecting compounds (e.g., similarity index threshold, area percentage, known bioactivity).
4. Documentation:
- Clearly document the methods used for identification and classification to ensure reproducibility and transparency.
By following these steps, you can systematically identify the classes of phytochemicals, choose which repeated compounds to include, and decide on the most relevant compounds for your manuscript.
you first obtain the mass spectra of your sample through the GC-MS instrument. Then, you match these spectra against those in the NIST library to find potential compound matches. The library provides information on the compounds, including their chemical class. Finally, you confirm the identity and class of the phytochemicals by cross-referencing the retention time and mass spectra data with known standards or literature values. It’s important to integrate all available data to ensure accurate identification.
You need to match those mass Spectra in your test ingredients or sample with those in the NIST library to obtain the chemical compound that are similar.
In addition to the above responses, when the same compound is repeated more than once, consider the one with higher match factor.
- Badges
- Science topic
- Similar topics
- Phytochemistry
- Extracts