Chromatography Forum

Hi,

Me again, got a little problem. I got the LC-MS data for my sample and there are 3 abundant compounds, showed up in the LC profile. As I could not find any mass spectrum library for flavonoid, I just matched the Molecular Ion m/z of second compound with the mass of compounds available in the flavonoid database and found a good match, After that I used the chemdraw software, deleted some portion of the compound, matched the fragment with the base peak. I want to know If that is the right way. But for both of the other two peaks, spectrum shows same molecular ion at 1151 m/z and two peaks at 279 and 900. with the variation only in the intensity of 279 and 900. How I go to predict the fairly right structure. As my course gets over I really don't have the time to go for NMR and I do not have that much compound of good purity. Please give me some suggestions. Thank you.


Shamphilics

The correctness of this approach depends on 1) how much informaiton you have about the sample to start with and 2) what you do to confirm your guess.

If your instrument provides accurate mass information, you can limit to a limited number of molecuar fomulae based on the accurate mass alone. Examination of the isotope cluster of the molecuar ion for isotope rations can help narrow this down further. If you have CID or MS/MS information, you need to be sure that what you are proposing agrees wiht the fragmentation you observe.

Knowledge of the sample can reduce the list of suspects.

Unless you have reduced all posibilities to one by this point, you still have further work to do. One of the best techniques is to obtain some authentic material and see if it has the same retention and spectral characteristics as the unknown.

What flavonoids do you expect to see? If you're working in material that is well-documented to contain quercetin glycosides, for example, and you find something that either (a) fragments in MS2 to 303 (hydrogen adduct of quercetin) via losses of sugar moieties, or (b) exists in simple LC-MS as a set of ions from 303 to the molecular ion, differing in mass by sugar moieties or combinations thereof, then you're probably right. If you just have a peak that is the same mass as a flavonoid in a crude biological extract, that's fairly weak evidence on its own.

Are you doing MS2, or looking at source fragments?

You can also look at the PDA data, if you have any, and check they look like flavonoids.

At these molecular weights, I assume that you are using electrospray, which means that if you are looking at single-charge ions, you are looking at protonated molecules. This means that you need to subtract 1 from the observed value to get a mass of the molecule. You probably need to subtract 1 for the hydrogen mass defect. Look at the intensity of you X+1 peak relative to the X peak. Depending on the type of mass spectrometer you are using you should resolve these two peaks. As was already pointed out, the molecular weight in your flavonoid database is going to be an average mass; therefore you need to try to come up with an elemental composition (don’t forget the Nitrogen Rule). This is best done with an accurate mass measurement, but you might be able to use the relative intensities of isotope peaks. Good luck.