The calibration equation is derived from the relationship of kinetic energy to mass and velocity. Rearranging Equation 1 to solve for velocity, v, gives the relationship in Equation 2. Velocity is distance divided by time or d / t. Substituting d / t into Equation 2 and solving for t produces Equation 3.
KE = 0.5mv2 [Eq. 1]
v = [2KE/m]1/2 [Eq. 2]
t = m1/2 * d/[2KE]1/2 [Eq. 3]
Distance and KE are assumed to be constant and can be replaced with A. The relationship between t and m1/2 is linear and an intercept is added to produce a simple equation for a straight line (Equation 4).
t = Am1/2 + B [Eq. 4]
Solving the calibration equation requires two standards. The equation is solved for the two unkowns A and B using the known m/z ratios and their flight times. The current technology permits mass measurement accuracy of 10 parts-per-million (ppm) or better for peptides in the range of 500-5000 m/z . Mass measurement accuracy of 100 ppm or better can be obtained for proteins in the range of 5000-30000 m/z .
Time-of-Flight Mass Spectrometry – Instruments and Applications in Biological Research by Robert J. Cotter  is an excellent resource for learning the basics of TOF mass spectrometry.
 Edmondson, R.D., Russell, D.H., J. Mass Spectrom., 1996, 7, 995-1001.
 Watkins, L.K., Bondarenko, P.V., Cockrill, S.L., Song, S., Barbacci, D.C., Russell, D.H., Macfarlane, R.M, J. Chrom. A., 1999.
 Cotter, R.J., Time-of-Flight Mass Spectrometry – Instruments and Applications in Biological Research; American Chemical Society: Washington, DC, 1997.