Three methods of operating an ion trap mass spectrometer (ITMS) were investigated for the determination of quantitative information by combined capillary GC/MS and GC/MS/MS. Separate regression lines for a hexynone drug were examined by using both unlabeled and stable-isotope-labeled internal standards. The ITMS modes of operation examined were (1) the full-scan, rf-voltage-only mode, useful on ion trap detectors as well as on the ITMS, (2) a scan using combined rf and dc voltages (rf/dc) for mass-selective storage analyses, and (3) rf/dc followed by collision-induced dissociation. Results of over 200 analyses in the 0.1–10 ng on-column range, with 5 ng of internal standard, showed that the unlabeled internal standard, separated by retention time on the capillary GC column, gave the best relative standard deviations (less than 5% over the range) and linear correlations ( r 2 typically > 0.9992).