[RASMB] Low s value peaks

[John Correia]

Peaks in C(s) do not necessarily mean that it is an actual peak in the
sample - spurious peaks or shifting peak positions in sedfit is caused
by the fact you are fitting the data to linear combinations of 100 s,
common f/fo values.  This is remarkable overdetermined and the actual
amplitudes you get are not necessarilly reliable.  If they are not also
supported by a noninteracting species fit then they very well may be due
to the nature of a c(s) fit.

Yes, sedfit can sensitively pick up small zones, but I never trust them
unless I repeatedly see it in multiple samples and if possible can
verify their presence by direct boundary fitting to a more realistic
model, ie fewer parameters.


-------------------------------------------------------------------
 Dr. John J. "Jack" Correia
 Department of Biochemistry
 University of Mississippi Medical Center
 2500 North State Street
 Jackson, MS  39216
 (601) 984-1522                                 
 fax (601) 984-1501                             
 email address: jcorreia at biochem.umsmed.edu     
 homepage location: http://biochemistry.umc.edu/correia.html
 dept homepage location:    http://biochemistry.umc.edu/
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>>> "Jones, Samantha" <samantha.jones at imperial.ac.uk> 01/23/04 11:20AM
>>>
Hello all
I have been trying to analyse some interference data on Sedfit and
have
been repeatedly seeing a large 'half' peak at very low s values on my
s
value distributions.
On the continuous c(s) distributions after fitting to range of 0.1s to
10s the distribution line starts at c(s) values of 1.5 to 0.5 on 0 on
the x axis, dropping to 0 on the y axis by 0.1s value. This is still
the
case after changing the parameters to 0.01s to 10s. 
The buffer used at first was 10mM NaAcetate, 0.2% Azide and 2mM DTT pH
4. At first I thought it could be the DTT but I saw the same thing
using
a sample in a buffer 10mM Tris 10mM Na Acetate, 0.2% Azide no DTT pH 8.

I have seen this spinning at 30K and 50K for about 16hours.
 
Could Azide be the problem? I don't expect either sample to be
contaminated, however anything of this size would have been missed by
the SDS-PAGE gel run on both samples.
 
Thank you
 
Samantha Jones
Samantha Jones 
MRC Prion Unit 
St Marys Hospital 
Norfolk Place 
London 
W2 1PG