matching MW of spots and protein identity

Johan de Boer jdboer at
Tue May 7 19:20:55 EST 2002

Hi all,

I have a question regarding matching the MW of a protein spot found on a 2D 
gel with that given for that protein by it's identity after identification 
by MALDI. I have seen several instances where there is a significant 
discrepancy, with the gel spot generally being too small, such as 50 to 
200%. Yet, the matching MALDI fragments of amino acid sequence are spread 
over the whole protein, so the entire sequence should be there. What can 
affect the running of proteins on the gels that much? As an example, we 
find very good matches for glutathione S-transferase (covering parts all 
over the protein) for a spot at gel position of 17kD while it is supposed 
to be 26kD. Others are even more off.

Johan de Boer
University of Victoria
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