Chromatography Forum

please recommend good books for MS data interpretation for smaller molecules and structure elucidation etc.



Thanks.

I assume by the fact you're posting in LC that you are looking for a book on LC-MS CID fragmentation.

Sadly, although there are many good books on GC-MS fragmentation, I do not know of a good one for low energy LC CID. I wouldn't normally reply to a question that I can't answer positively, but no one else has written, and there is a reason why you might not find the book you're looking for:

At the low energies used in CID, the statistical likelihood of a bond containing enough energy to break in EI-style is very low, so ions have longer life-spans (look up QET theory if interested). However, if they can undergo internal reactions and rearrangements, they need less energy to fragment, and with their longer lifespan and lower energy, this is the more likely route for fragmentation. To undergo such rearrangements, they usually have to twist round into a particular conformation so that the right groups are aligned appropriately; this is slow but works at low energy. Unfortunately, these rearrangements depend very strongly on the chemistry and shape of the individual molecule. They are not so easily predicted as the "simple" processes of fragmentation following EI.

So to understand CID, all the normal rules of organic chemistry apply, with the exception that you are working in the gas phase, so solvent influences are absent.

Interpretation of mass spectra (of known molecules) is much easier than structural determination. I get a bit irritated by papers claiming structural identification on mass spec alone. Usually they are either (a) retrospective, starting with a known molecule and proving they could have identified it, honest Guvnor, even if they hadn't known, or (b) they come from labs who have very detailed knowledge of one particular very narrow class of compound, and they relate entirely to this sort of compound. Group (a) are basically fraudsters, and group (b) are so specialised that outside their field, unfortunately, what they do cannot be generally applied.

A book could be written, but it needs a real expert, it would be very fat, fascinating, and hard work. It might not advance the cause of human knowledge in a very practical way, though. If anyone has written it, or read it, I'd also like to know.

Thank you

What I would like to see is a huge data base of small molecule CID spectra (both polarities) and retention factors in 2 or 3 different modes of separation... There are some metabolomics initiatives that trying to do that but there efforts fall short still. I am thinking of all the compound libraries that can be found in universities (i.e. organic synthesis labs) and pharmaceutical companies...

It would have been fantastic to have such a database and probably easier to make fragmentation rules etc...

there are still some issues to clear up. For instance ion trap CID will look totally different to triple quad CID (because of the issue of whether daughter ions are further fragmented).

I'm watching Metlin with interest.

I think rules will only emerge once computers and software are powerful to deal with 3d structural calculations on molecules (finding the most likely configurations etc.) as a routine matter. In a molecule
A-wobblychain-B-C
a fragmenation reaction involving intramolecular attack of A on B or C depends enormously on the way in which A can move around relative to B and C.