[M-2] fragments in peptide LC-MS-MS

[Lindsay]

Hi,

I'm trying to run protein digests on my Bruker HCT ion trap, with auto-MS2. The chromatograms look ok (as far as I can tell!), but I'm getting really poor quality MS2 data (and therefore rubbish Mascot results).

I've noticed recently that a high proportion ( ~80%) of the MS2 spectra consist of M- ~2 Da ions (compared to the precursor ion), and not a lot else. The precursors are usually designated as being 2+ and the products 1+, so I'm seeing (e.g.) 710 (2+) fragmenting into 708 (1+).

Has anyone else come across this? Any help would be gratefully appreciated!

Best wishes,
Lindsay.

[Kostas Petritis]

I have never noticed anything like what you are descirbing (i.e. very unusual problem)... my suggestion would be (if you haven't done it already) to recalibrate all the parameters of your ion-trap (i.e. not only fragmentation but isolation etc...).

Also, just double checking:

What is the +2 m/z mass spectrum of your example; is it 355 or 356?

Are you using the recommended collision energies for peptide fragmentation?