I need suggestions in programming the fraction collector. My problem is that the impurity peak is too close to the main peak, if I time the fraction collection I might miss it each time I prepare new mobile phase.
Thank you for your help in advance.

You need to know the time delay between the signal in the detector and when the sample shows up in the fraction collector. The time can be determined by disconnecting the column and injecting a dye. Look for the delay between the signal in the UV and when you see the dye at the end of the tubing that goes into the fraction collector. You may need to work at a detector wavelength way off from the maximum UV absorbance. Once you know the time delay at a particular flow rate, you should be able programm the fraction collection accordingly.