First, after 4-color upgrade the FL3 channel has a 670LP rather than 650LP
filter. This will probably be BETTER for PE/Cy5 in that PE emmission will be
slightly reduced in FL3. There are no other issues in 3-color applications.
Second, the system HAS inter-beam compensation. The compensation value for PE/
Cy5 conjugates is quite high because of the direct red excitation of Cy5. I
have used comp values like 60% on only one instrument - also only two PE/Cy5
conjugates from only one vendor - "your mileage may vary". Very bright PE/Cy5
conjugates could thus be a problem but dimmer ones seem OK. A strategy where
the PE/Cy5 reagent subsets the APC-positives would be more robust than vice
versa.
Conclusion, PE/Cy5 can be used for 3-color as always - PE/Cy5 is usable, but
PerCP has compensation advantages, in 4-color applications.