[RASMB] downward sloping baselines or "i no longer have much hair left to pull out"

[Peter Schuck]

Hi Jack,
we have encountered similar problems in the past, usually with 
interference optical data where either our collaborators didn't give use 
the right buffer, or I picked the wrong one, or the buffer exchange 
didn't work out.  SEDFIT currently has models for evolving baseline 
curvatures arising from (unmatched) sedimentation of buffer components 
in the reference sector.  In our hands, this has worked very well in 
most cases.  This was not yet publicly released and announced, simply 
because we didn't have the time to write it up.  I can walk you through 
how to use it. 
Peter



Jack Kornblatt wrote:
> I have checked the RASMB archives and there does not seem to be 
> anything on this particular subject.
> The problem is not the XL-I; the problem is an overly complex sample 
> and reference.
>
> The sample contains a protein that absorbs at 290 nm as well as a 
> ligand that absorbs at 290 nm.
> The reference contains just the  ligand. Both are in matching buffers.
>
> The first scan: The baseline absorbance starts below zero and becomes 
> more negative at higher radius.
> Scan 100: The sample has almost sedimented completely giving the 
> baseline absorbance what appears to be a "bow".
> Scan 200: The sample has sedimented completely and the absorbance is 
> well below zero. It is more negative at high radius than low radius.
>
> The problem is clearly the sample. I have not run the "control" in 
> which the sample compartment contains no protein but does contain 
> ligand; reference compartment contains no ligand.
>
> This problem must have come up in the past. Needless to say, all 
> analyses are feasible but they are not likely to be correct. I'm at 
> wits' end.
>
> thanks for any help you can give. i am attaching an xlgraph of the 
> three scans.
> jack kornblatt
> ------------------------------------------------------------------------
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