[M-2] fragments in peptide LC-MS-MS
Posted: Fri May 25, 2007 10:07 am
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.
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.