by
lmh » Fri Oct 18, 2013 3:39 pm
... but I'd urge caution in any promise to find the structure of an unknown compound using LC-MS alone. LC-MS fragmentation is weird, much more influenced by conformational possibilities of a molecule than EI fragmentation. Huge intramolecular rearrangements can be possible. Depending on your instrument, the fragmentation spectra can be fairly information-poor too (some compounds are just hard: for example, at my fairly amateur level, it's very easy to spot glycosylations, but very nearly impossible to differentiate between which of 5 hydroxyl groups on a compound happens to be attached to a sugar; for some classes of compounds there are good papers demonstrating that different isomers actually fragment identically, and misleadingly). And the libraries are nowhere near as good as the well-established EI libraries, although they're growing rapidly. Accurate mass is great, but even with quite decent accurate mass, say 1ppm on a molecule of 600Da or so, you are likely to have multiple candidate formulae, especially if you can't rule out strange elements.
I always warn people who want to identify true unknowns by LC-MS, even with good accurate mass, that they may, ultimately, be forced to purify enough for NMR. When I read papers where people claim full identification, it often turns out they are experts who've spent their lives on the particular class of compound they are identifying, and possibly know quite a lot about which compounds are possible and which are not.
That's not to say you shouldn't try. You can certainly get some useful information: likely presence of obvious groups, possible elemental composition, possible similarities to already-identified components of your mix. If you're lucky, you might even get a (believable) match on accurate mass against one of the nascent libraries, be able to source the suspected compound, and check its chromatography and fragmentation match the unknown peak, and then you've got pretty reasonable evidence without actually having to interpret anything. But you'll have to be veeerrry lucky! I wish you this good luck!
