Hi Guys,
A couple of questions with which I need to tap into the collective experience.
We're using a Finnigan LCQ electrospray (with a nanospray module) to do
some protein analysis and being new to the LCQ there are one or two
problems we're having difficulties with. Firstly, I've been using the
Zoomscan feature to check the charge state of a number of tryptic peptides
and have been having difficulties getting interpretable results as the
signal flicks between +1 and +2 readings sometimes going as high as +3. The
signals I am looking at aren't always the strongest in the spectrum (NL
approx 10e-3/-2) and usually vary quite markedly in their intensity.
Subsequently when I attempt MS/MS on the signal, however much I manipulate
the isolation width (generally between 1.0-3.0) I always seem to get some
'stray' signals either side of the main signal. For instance I was looking
at the fragmentation of a peptide of m/z 938.6 and the parent signal seemed
to be coming from m/z 937.0 - 938.0. Is that sort of variation
normal/acceptable? How do I get a sensible reading from the zoomscan? Most
of our samples are cleaned up using Zip Tips prior to analysis.
Secondly, having had some zoomscan results indicating a +1 charge state,
when I perform the MS/MS on the same ion I still get peaks at higher m/z's,
suggestive of a higher charge state. Are there any diagnostic tests I can
perform to check the performance/calibration of our machine?
Thanks and regards,
Derek Bradley
Department of Medicine
UCL
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