Are there software to predict fragmentation pattern of a derivatized molecules?
11/9/23
Dear Teresa,
Usually, when a GC/MS is installed in a lab, the MS software package comes w/ a library of spectra. When a peak appears in the GC profile, you can display the analyte's fragmentation and have the MS's library identify it for you. In my experience, the library will list 10-20 possibilities for the analyte and rank them percentage-wise in descending order of the accuracy of the identity. It's the MS computer's way of telling you what it "thinks" the unknown is. If your MS will do this, you can purchase small amounts of the most likely and try running them on your GC/MS and see how well they match up. You can also try running it on the GC/MS under different parameters and see it the identity holds up.
I hope this information helps you.
Bill Colonna Dept. Food Science & Human Nutrition, Iowa State University, Ames, IA USA [email protected]
Databases such as Wiley, and NIST also include the EI/CI fragmented spectra of derivatized molecules...MS to the n experiments will also be helpful for structural elucidation in case in-house developed/local or global repository databases cannot annotate the compound.
If the compound is a not in NIST nor Wiley data bases? How can I elucidate the novel compound. Do you know software that can perform fragmentation pattern of derivatized molecules ?
Yes, there are a couple of in-silico fragmentation tools...
I am using Massfrontier software from Thermo to elucidate compounds analyzed at ESI-Orbitrap-MS. This tool can also be used with EI/CI fragmentation whether the compound is derivatized or not. Very useful, practical, and versatile software, and MS to the n option also exists...
Here are the known other alternatives;
- Metaboscape uses In silico fragmentation using implemented MetFrag functionality from Bruker. It also evaluates the CCS values for compound annotation.
- MSfinder
- Metfrag
- SIRIUS
- CFM-ID
- CSI:Finger ID
I do not have much knowledge about the use of these abovementioned softwares and I am not sure that they can serve reliable predicted EI spectra...
BTW, Even if you match your experimental spectra and theoretical spectra with a high score, NMR-like characterization may be requested for confirmation...An orthogonal approach is generally needed to fully validate the novel compound. Without database confirmation, it is a bit of trouble to take general acceptance for molecular elucidation...
I hope these are helpful for your case...
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