Hi Derek:
I recommend that you use an AGC target value of 3E6 for the zoom scan when
analyzing peptides. The default target of 1E7 will space charge the trap and
produce unreliable charge state assignments. At this value the zoom charge
state assessment algorithm should work well even with low signals.
A between scan variation of 938.6 and 937.0 - 938.0 seems too large. I would
want to look at the data.
Your observations of "stray signals" make me doubt the instrument
calibration. I recommend recalibration whenever there are doubts about
calibration accuracy. (Remember that with LCQ class instruments the standard
calibration covers much more than mass assignments (e.g. resolution,
waveform, ejection RF,...) Monitoring the accuracy of the Full Scan MS
masses is not an adequate assessment.
Regarding diagnostic tests:
Run (from Tune) Diagnostics - All - Everything and print report. Send the
report to our Tech Support Group if there are any failures.
Then perform the standard calibration. If there are any failures copy the
calibration dialog to a word document and send it to tech support.
Bill Mahn
TMQ Technical Support
T: 800-685-9535
F: 561-881-8436
E: Bmahn@thermoquest.com
----- Original Message -----
From: "Derek Bradley" <Derek.Bradley@ucl.ac.uk
<mailto:Derek.Bradley@ucl.ac.uk>>
To: "Recipients of ABRF List" <abrf@aecom.yu.edu <mailto:abrf@aecom.yu.edu>>
Sent: Tuesday, November 14, 2000 11:36 AM
Subject: MS: Zoomscan and isolation widths on LCQ
>
> 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
>
Bill Mahn
TMQ Technical Support
T: 800-685-9535
F: 561-881-8436
E: Bmahn@thermoquest.com
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