I am currently trying to develop isocratic HPLC conditions for a new sample. However I keep getting 2 large negative peaks. I would like to know how one gets a negative peak using a diode array detector using the following conditions:

Flow rate 1 ml/min
injection volume 10µl
Column temp 40°C
DAD just collecting at 254 and 275 nm

I've tried 75% methanol/25%water for a mobile phase as well as 50% acetonitrile/50%water. The sample is made up in acetonitrile. I would be very grateful for any insight on why/how this could be happening.

Normaly your chromatographic system shouldn't create any artifacts with the mobile phase and wavelength you use (if your products are not eluted in the void volume; what is the retention time of your peaks?).
Try to make your samples in the mobile phase you use each time. Are you sure that your samples absorb in the upper wavelengths?
The only thing that I can think of is (if you just put together your HPLC-system)that your 1V output has been reversed so everything positive response deviation gives a negative peak.

I'm not sure which model detector you are running, but on some models, you can set a reference wavelength to compensate for RI change when running gradients. I have seen analysts accidently set a reference wavelength that corresponds to significant absorbance by the analytes, in which case negative peaks may results.

Just an idea. Good luck.

Are you getting negative peaks INSTEAD of positive, or as well?

I was getting negative peaks and positive, however when I altered the reference wavelength as suggested above the responses were positive. Thanks for the help!