[Protein-analysis] question

Kate Chabarek kchabare at cats.ucsc.edu
Thu Jul 13 18:32:24 EST 2006

I am trying to isolate 100 ug of a transcription factor in order to determine its phosphorylation sites. 
I unsuccessfully tried a lot of different protocols and ended up, crude as it sounds, doing a huge immunoprecipitation under denaturing conditions. 
I get one band of the correct size by silver staining, zinc-imidizole staining, and Western blotting. Hooray-except that the A260 of the HPLC-separated sample is about 60% larger than the A280. I ran an agarose gel and don't see any DNA there. Also, I can't confirm its identity by mass spec. I don't know what this band could be if it isn't my protein of interest~it doesn't match the size of anything else in my immunoprecipitation. Because it is very low-abundance and has no enzyme activity it is hard to quantify. I am wary of sending it out since I can't confirm what it is and because of the weird A260 result. 
Has anyone had this experience, and what did you do?
Thank you.

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