cell cycle analysis : move 2n peak?

Hello,
I have a question about cell cycle analysis using IP :
a researcher is interested in studying the effect of drugs on cell cycle.
He is doing IP staining on cells after different treatments.
I adjusted the peak 2n at 200 with the control cells but with some 
conditions the peak 2n shifts a little bit (higher or lower depending on 
the condition) so my question is :
do I have to adjust the peak at 200 for each conditions (so we can do an 
overlay after) or keep the same cyto settings and adjust the marker?

Thank you for your answers

Julie Bertout
cytometry lab
Institut Pasteur de Lille
1 rue du professeur Calmette
59800 Lille
France