We have performed aircraft-borne intercomparison measurements of acetone and acetonitrile using two different mass spectrometric techniques: A Proton Transfer Reaction Mass Spectrometer (PTR-MS) operated and developed by the Institute of Ion Physics, University of Innsbruck, and an Atmospheric Pressure Chemical Ionization Mass Spectrometer (AP-CIMS) operated and developed by the Max Planck Institute for Chemistry, Mainz. The two devices were employed for atmospheric trace gas measurements over the Indian Ocean on board the National Center for Atmospheric Research C-130 research aircraft during the Indian Ocean Experiment (INDOEX) intensive field phase in February and March 1999. Both instruments use reactions of ions with atmospheric trace gas molecules and mass spectrometric detection techniques for the determination of trace gas concentrations. For the detection of acetone and acetonitrile, both mass spectrometers operate in the positive ion mode and detect the protonated species of these compounds. One difference of the two systems is the operating pressure of the reaction chamber, where the ion molecule reactions take place. While the PTR-MS uses a low-pressure (2.2 hPa) drift tube, a much higher pressure of 300 hPa is used by the AP-CIMS. Other differences are the determination of background concentrations and the calibration procedure. The AP-CIMS uses a charcoal filter, and the PTR-MS uses a Pt catalyst. For the AP-CIMS an on-line calibration is necessary, which is performed during the flights. The intercomparison measurements described here were carried out on two research flights along a north-south transect along 73 ¿E between 6 ¿N and 8 ¿S. Altitudes between 100 m and 6500 m above sea level were covered. Backward trajectory analyses indicate that the sampled air was taken from polluted air masses originating from Indian and the Bay of Bengal as well as from remote southern hemispheric air. During the two flights on February 20 and 24 the position of the Intertropical Convergence Zone was located around 1.5 ¿S in the investigated area. The measurements of both instruments of acetone and acetonitrile indicate a strong gradient in the boundary layer and a weaker one in the free troposphere. The values measured by the PTR-MS are higher than the ones by the AP-CIMS, but are within the combined error range of ¿20--30% for each instrument. Acetone mixing ratios up to 2.5 parts per billion (ppb) and acetonitrile up to 0.4 ppb were measured in the northern hemispheric boundary layer. The measurements in the free troposphere give values between 0.3 ppb and 1.0 ppb for acetone and 0.12 ppb and 0.3 ppb for acetonitrile. ¿ 2001 American Geophysical Union