A new method for quantitating adenosine concentration by capillary gas chromatography-mass spectrometry-selected ion monitoring (GC-MS-SIM) has been developed and used as a reference method for evaluating a newly developed radioimmunoassay (RIA) for adenosine. Details of the GC-MS-SIM method are presented, along with the comparative results and uncertainties of both methods. General considerations in the statistical analysis of method comparison data are discussed with particular reference to studies using quantitative mass spectrometry as the standard method; the adenosine methods are used as specific examples in this discussion. Simultaneous estimation of the y-intercept and slope of the least squares regression line relating the results of the two methods using the 95% joint confidence ellipse demonstrated the absence of either constant or proportional error between the two methods. The relatively small uncertainty in the GC-MS-SIM measurements had no significant effect on the linear regression. Random error between the two methods was detected, and was estimated by the coefficient of variation in the RIA data as ten percent of the RIA value.