I did GC-MS for my samples. I got few new peaks which were absent in the substrate control. What could be the possible approach to analyze those peaks which may correspond to the novel compounds (i.e, neither commercial standards are available nor has any record in the MS database). Kindly suggest
Hi Pranav, it depends on the type of Instrument you are using. If nominal mass EI-TOF-MS you can use Tools to predict the compound class at best if you don't find a good match in available libraries. If your data is high Resolution APCI-MS for example there are several tool which allow to predict at least the sum formula (look into e.g. R package InterpretMSSpectrum or MSFinder for a start). Bests, Jan
Hello Pranav, what kind of mass spectrometer (quadrupole or TOF) and what kind of ionization (EI or CI) do you use? With TOF you can determine the exact mass of the elemental composition of your new compounds. EI provides more structural information through fragmentation reactions, while CI (gentler ionization) provides you with molecular weight information. The rest is an interpretation of the mass spectrum. I recommend the book by Fred McLafferty (https://books.google.de/books/about/Interpretation_Of_Mass_Spectra.html?id=xQWk5WQfMQAC&redir_esc=y). Regards Markus
Hello Markus
Ionization mode is EI, positive ion mode and the mass spectrometer is quadrupole MS
Hello Pranav,
EI is quite good, but a quadrupole is only conditionally suitable to determine elementary compositions. Okay, you can derive statements about chlorine and bromine from the isotope pattern, the number of sulfur can be derived from the M+2 peak, the nitrogen rule makes statements about the number of nitrogen (even or odd), from the M+1 peak you can estimate the number of carbon atoms, fragmentation patterns give you information about the substance classes (e.g.. mass difference of 14u indicates alkyl chains, m/z = 91 tropylium cation is typical for aromatics), but an exact mass is of course particularly helpful in determining the elemental composition. Agilent offers in this context a software (http://cernobioscience.com/), with which one can increase allegedly also the mass accuracy with quadrupoles. I have not yet worked with it and can therefore make no further statements. You can also post the mass spectra of your compounds. Let's see what the community has to say about the spectra interpretation. Regards Markus
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