values are used for calibration), the calibrated masses will be too high. This is understandable since ions will generally be ejected slightly after their resonance conditions have been met, and the frequency in these experiments was scanned from low to high (high to low mass). However, when these values are corrected for the mass-dependent ejection delay and incorrect inputs for trap parameters (e.g. V0-p), the calibration error decreases to ~10–600 ppm, which is in reasonable agreement with the typical mass accuracy of a linear ion trap, ~50–100 ppm. Some of the calibration error is due to the mismatch between the LTQ’s data system, which records a constant 100 points per integer mass, and the variable scan rate of the secular frequency scan. This results in one data point being acquired every ~0.37 ms. More error can be attributed to the necessity of choosing a built-in scan function, in this case the Ultrazoom scan, to minimize the change in the rf voltage. However, our calculations took this into account by incrementing V at every time step. Even with these difficulties, the calibration accuracy was always less than 0.1%, which is sufficient for determining the integer masses of the analytes.