LC/MS advice and Info

[BrendaB]

This is one of those questions that may be too general to answer and i know it.... but please try anyway!

We need to ID peaks from some unknown compounds being produced by some microorganism that I see now and likely more in the future. So they can be small or larger molecules... and I can't narrow thing down any more right now.

One way to start getting a handle on this could be via LC/MS with gentle ionization technique that gives strong parent ion ... Or do i want a strong technique to have better fingerprint for spectrum match?

But although I have a lot of chromatography experience, no place I've worked has used LC/MS. So I have a lot of research to do and I'm hoping some here might help point me in the right direction.

There are various ionization techniques (with electrospray looking to be most common) and all sorts of mass detector configurations with LC-TOF being the one with the broadest mass range... though I suspect that won't be high resolution for lower molecular weights.

So my other questions are:

1) What are the best ionization and mass detector type options that should be considered for this type of work?
2) What are their relative strengths and weakness?
3) Ballpark, what would they cost (not considering the HPLC)
4) Are their other vendors besides Agilent and Waters that should be considered.

Thanks,
- Brenda

[Gaetan Glauser]

Hi Brenda,

For unknown compound identification, the most appropriate mass specs are those enabling either high resolution or MSn, or both. Ion traps perform MSn at nominal mass, TOF allows for high mass accuracy, and Orbitrap and FT-MS for both. My favourite instruments for this type of work would be either Orbitrap or latest Q-TOF, which cost between 500-1000 k$. There are 5 main vendors that you could consider: Waters, ABSciex, Agilent, Thermo, and Bruker.

The mass range is not the most important parameter to be considered since electrospray produces multi-charged ions.