Hi, Scott -

Can you tell us a bit more about your system?  Do you have a high-resolution instrument?  Empirical formulas depend on exact masses; maybe what you're after are structural formulas?  You mention fragmentation, but indicate that you have an LC-MS instrument rather than an LC/MS/MS instrument; are you seeing in-source fragmentation?

You're correct that it's unlikely that there's a library of mass spectra for heavy-metal-containing compounds; perhaps you can create one. 

So - bottom line - I (although others may) don't know of any software that does what you're after.

You may ultimately be better off - labor-intensive as it will be - to manually interpret your spectra until you get a good sense of your compounds' mass spec behavior and then either creating your own library or perhaps even writing your own software.

It's always a risk to rely too heavily on software until the system itself is well understood.  I understand your original question, but I do think it's better to work first by going through your spectra compound by compound and peak by peak until you feel that you understand.

Best.

Pete

Hi, I sometimes use ACD/MS Fragmenter. It provides a list of possible fragments. However, the isotopic profiles of these ions are not included (at least this option is not included in my version from 2009...)

http://www.acdlabs.com/products/adh/ms/ms_frag/

Hi Pete,

I have been using a high res ESI-MS, and I believe that the fragmentation is occurring during the ionization (even though ESI is considered "soft"). I think that you are probably right, and I will need to attempt manual interpretation,  as writing such software is likely to cumbersome for me to attempt at the moment. I will attempt an assignment based upon the most likely fragmentation. 

Thanks for your help Pete. Cheers,

Scott