[RASMB] What is wrong with my XLA?

[Borries Demeler]

> 
> Fellow centrifugationistas, 
> Attached find two .png files of 1) two sample meniscus regions from data
> collected in the intensity mode at 280nm, and 2) the resulting data from
> one of these samples after time independent noise subtraction. 
> almost certainly there is a problem with my slit assembly, resulting in
> the menisci which defy fitting. My question is, is the very anomalous data
> (which does not fit via van Holde-Weischet analysis)a result of ONLY the
> meniscus jumping about, or is there perhaps another cause superimposed on
> the slit assembly? 
> Finally, there is a noise signature at 6.35cm in all sectors of all cells
> always with this machine. I have cleaned the glass filter in the bottom of
> the rotor chamber that protects the lamp, and blown some compressed air
> gently into the slit in the monochrometer assembly. Neither act has removed
> the offending noise. Any further suggestions for removal are appreciated. 
> cheers, 
> steve

Steve,

I am with John on the meniscus issue - can you plot the first, middle
and last scan in three different colors, it would be nice to see if
there is a pattern to the meniscus drift.

Secondly, the scans in the velocity scan seem to jump around and
apparently seem to have different scalings. Assuming you collected scans
from both reference and sample channel, are you sure that the absorbance
of the sample plus baseline absorbance in the reference cell did not
exceed 0.5 OD? It almost looks like it rescaled on you. If not that,
perhaps it was acquired at different wavelengths. The scans you show do
not show a regular velocity pattern. Something is screwed up either with
your expt.  design or your instrument, there is not enough information to
determine which.  You should run some diagnostics on your machine and call
Beckman service for assistance - it is not clear what is going on here,
but too high a concentration in the reference channel will cause a reset
of the gain settings for the PM tube, and you want to avoid this. Even if
your sample OD is 0.3 or less, if you have baseline absorbance from buffer
or reductants, this can seriously mess you up. I just assume you are not
running DTT in your sample, correct?

-b.