Jan,
We're doing this for one of our users. Cy3 can be measured using the FL2
detector. It wouldn't be my first choice (or my 2nd or 3rd or...) of a
conjugate to excite at 488 but it seems to work. Perhaps that's just
because their antigen is highly expressed, but I have no data with another
fluorochrome to compare.
This web page has spectra for CY3:
http://optics.jct.ac.il/~aryeh/Spectra/GIFs/Cy3.18.GIF
Good luck,
Neal Benson
-- Neal Benson University of Florida E-mail: neal-benson@ufl.edu