[RASMB] XL-I poor data troubleshooting

[Mark Agacan]

Hello,

I am having problems with the data being collected on my XL-I.  For all the samples I have studied lately, the rmsd has been 0.2 - 0.8, the residual bit maps show large contrast from black to white running in a diagonal across the whole data range, and the MW values output from SedFit bear no resemblance to what I have been  expecting.    

I have also noticed that the S-values just don't seem right:  e.g. cell 2 = 6.545455; cell 4 = 7.272728; cell 6 = 8.383839;
The repetition in the numbers after the decimal point are surely artefactual?  I've never seen a dataset consistently produce numbers like this.

I have used different windows and centerpieces in an attempt to get better data but to no avail.  My sample preparation is standard and the samples and buffers are standard, e.g.  50 mM Tris 100 mM NaCl.  All samples show up as distinct bands on gels with MW values as expected.

I recently had the radial servo replaced on my XL-I - could this or malfunctioning / poorly calibrated optics be to blame?  I will run a lysozyme sample (MW = 14.4 kDa) in the next few days in place of a suitable standard.  The residual bitmap and high rmsd makes me think that the optics may not be properly aligned and that they are imaging part of the walls of the centerpiece, instead of the sample.

It's not impossible that the samples actually really do have the mass and S-values as output, but I am highly suspicious, and the rmsd values are terrible.

Has anyone had issues such as this, and if so have you any recommendations or ideas that I can try in order to get to the bottom of this problem?

Best Regards,

Mark


_____________________________________
Dr Mark Agacan
Scientific Officer,
Division of Biological Chemistry 
and Drug Discovery,
Wellcome Trust Biocentre,
College of Life Sciences,
Dow St., 
University of Dundee,
Dundee, DD1 5EH
Tel: +44 1382 388751
Fax: +44 1382 345764
_____________________________________
The University of Dundee is a registered Scottish charity, No: SC015096