I am working with my students to obtain compound of interests from plants local to our region. My students want to use the compound for drug discovery. They already performed LC-MS in a local laboratory and produced .raw folders for each person data (which I believe those came from the instrument, Waters). In the lab and my students' training, they were instructed to interpret the data using ChemSpider to acquire the compound name and the inputs were the chemical formula. When I saw the compounds, I am not sure or familiar with the results as they came back with compounds that I am not sure if the compounds are from a plant (no sign of certain metabolite like phenolics, alkaloids, etc.).
Following a friend suggestion, I converted the folders to MzML files for further analysis. I ran the files to XC-MS and I acquired a folder with hundreds of compounds, still without formulas or names, but I believe those are interpretation of the peaks found in the compounds. How do I interpret the MzML files here so I can choose any significant compound structures and names for further analyses and simulations (e.g., molecular docking, etc.)?
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