What exactly are you trying to calibrate? Using 100% Methanol as "sample" is, well let's say a bit extraordinary. If we're talking about RP-HPLC, I doubt that that there's really a retention (!) time measurable.
If you're trying to do something like OQ'ing the autosampler, you should use a decent sample.
Nevertheless, some thoughts:
- What about the peak area? Is it also doubled? If the peak shape changed, the height might do as well without the actual area changing.
- Are the conditions EXACTLY the same (injection volume, mobile phase composition, detection wavelength, flow-rate, column)? All of these might have an influence on peak height/area...
I used the RP-HPLC for ester analysis. The methanol injection (peak appeared around 2.1 minutes) actually aims to check the stability of HPLC. I do this check in two steps, first check with methanol injection then compare the peak height with previous result (which is done around 1-2 weeks before) and check with injection of one of data point in calibration stage.
1. The peak area changed, (previous around 1500 mAU*sec, current around 2400 mAU*sec).
2. All conditions are EXACTLY the same.
Do you have any idea, why the peak height change?