I have LC-MS spectra of extract where I have the PDF format of the spectra. I sent my extracts to a company who provided me with the pdf only (Not the original file of the software). The library of that company was not able to identify most of the peaks. Now How can I identify the compounds? for example i am have attached a LC-MS spectra pdf file for your better understanding.
According to my experience, if you do not have the putative stsndard, you have to compare the fragmentation of your component with literature.
Or in Google schoolar, search for the name of your plant the word of esi and the number of MW and the fragmentation number.
First thing, you have to clarify if you have any information regarding your organism of interest. If possible, start with looking into literature of similar analysis for the same species, comparing previous studies with yours. Using instruments with high accurate mass (and considering 2-3 decimals) is possible to make a list of targeted compounds of interest. You would probably also be able to compare retention times, relatively for each compounds, though accounting for the difference in the methods listed in your reference (e.g. solvents, total running time, pressure, length of column etc). The best way to confirm your identification is then to use a standard compound, and measure mass and retention time with the same method used for your samples. You should then perform MSMS experiments to compare the fragmentation patterns with your standard, or with data from literature and database (from real samples or in silico). Very useful databases are Scripps institute METLIN (based on LC-QTOF) and GNPS https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp
You may not want to hear this answer, but unless you are looking at already-identified compounds which are in a library somewhere, you will be best off using LC/MS/MS to examine the components of the extract. This approach will allow you to see how each compound fragments, at least under the specific experimental conditions, and will give you a very good chance of identifying things. Of course, you should first go as far as you can with the LC/MS data and the suggestions provided by the others. Best of luck! Jim
It will be a bit difficult to find the identity of the compound with the data you are providing.
First, try to find the real mass of your molecules, checking if it has adducts (Na+, K+), the fragmentation of the compound if it's losing H20, and so on. In some cases you can check the isotopic distribution of your molecule, this gives some hints about Br Cl or other atoms in your compound.
Then, using the "real" mass of your compound, you can predict the molecular formula.
If you have other detectors like UV or DAD, you can obtain better information about the whole UV-spectra of the molecule or UV maxima. It is important to use the same column, gradient, and additives (acids) for the run, and also to run it without additives because the low pH will change your UV-spectra (in the databases people rarely specify if the data was obtained with additives or not).
After you gather all the info about the exact mass, UV-spectra, molecular formula, and the source taxonomy; you can use it to compare with different in-house libraries or commercial ones (Dictionary of Natural products, MarineLit, etc.).
As some people mentioned before, standards are super useful only when you know what you want to find.
Also, take into consideration that the only way to be sure of the identity of your compounds is through NMR analyses.
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