I performed some EMSA assays with very puzzling results. Although I'm sure that in the shifts there is my protein, I'd like to better characterize them.

Is it possible to excise the band of interest, perform on membrane tryptic digestion and then spot the matrix for the MALDI?

I've used 5 µg of protein extract and 30 or 100 fmol of biotinylated DNA and a positively charged nylon membrane for the blotting.