Dear Derek
The Bioexplore deconvolution software is a real mess. I have never been
successful deconvoluting peptide mixtures. As you have found, the result
is hard to interpret. You can get a good idea as to how bad this software
is by running a protein sample such as myoglobin. You get a great series
of multiply charged ions but when it deconvolutes, the correct peak is
there, but also you get all other possible forms including half-mers,
dimers etc and paks in between. Once it is told which the 'correct' peak
is, then things do improve if the signal/noise is good. Choosing the
correct peak means that you have to know the right one to pick of course!
In the mass calculation option, the software can operate in automatic or
manual mode. My experience is that it only works in the automatic mode if
the number of peaks in the series is small, so something like myoglobin
often does work, but proteins of mass >20kDa rarely do and I have to
manually select all the peaks in the series. Be aware that the SD given in
mass calculation result is WRONG, usually about 2-3x too low. With careful
attention , I have successfully deconvoluted protein mixtures, and in the
case of large proteins like BSA, only the deconvolution option will give a
mass value that is useable as the mass calculation page can't cope with
the broad peaks.
I get the impression that the deconvolution software was something of an
afterthought and no-one took the time to make it really useful. It's
capability is much less than where Micromass software was over 10 years
ago!
Len
>Hi All!
>
>Does anyone out there have experience with the BioExplore software for the
>Finnigan LCQ and it's spectrum deconvolution routine ? I'm new to the
>software and have been attempting to get to grips with it by running a few
>known samples and have run into a few problems.
>
>I've tried deconvoluting the spectrum for a mixture of known peptides and
>the initial deconvoluted spectrum makes no sense, as the masses which I know
>the peptides to be do not appear amidst the jumble of artefacts. I've tried
>inputting the masses at the "Known Masses" prompt but it makes no difference.
>I've also tried accounting for various adducts with no success. Convoluting
>back to get the cleaned up spectrum just yields a sequence of peaks at odd
>m/z's.
>
>It's particularly annoying as on the unconvoluted spectrum I can see a
>range of clear peaks, all of which can be accounted for by the basic charge
>states of the component peptides. So why can't the deconvolution process
>clean up the spectrum ?
>
>Anyone there help?
>
>Cheers!!
>
>Derek Bradley
>Dept. of Medicine
>UCL
>London
*********************************************************************
Dr Len C. Packman
Assistant Director of Research
Protein and Nucleic Acid Chemistry Facility
Department of Biochemistry
University of Cambridge
80 Tennis Court Road
Old Addenbrookes Site
Cambridge, CB2 1GA, UK
Tel: +44 (1223) 333639
FAX: +44 (1223) 766002
e-mail: lcp2@mole.bio.cam.ac.uk
Visit my WWW page at http://www.bio.cam.ac.uk/proj/adr/PNAC/pnac.html
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