this is what i have been trying to do.

i have tagged N-term lysine of a synthetic 3KDa peptide with Cy3 . now i tried using 3KDa cut off centricons from millipore to remove free dye molecules. seems like it is not working. next i tied analyzing my HPLC fractions on mass spec. HPLC showed multiple peaks,mass of some fractions did not make any sense , as neither did they fall into labelled peptide (single or doubly labeled) nor into un labeled fraction.

what best can i do to get purified labeled peptide?

thanks

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