During TexAQS 2000 ambient air samples were analyzed on-board the NCAR Electra aircraft for volatile organic compounds (VOC) and peroxyacetyl nitrate (PAN) by two independent methods: 1) two in situ gas chromatographic systems, operated by NOAA's Aeronomy Laboratory and NCAR's Atmospheric Chemistry Division, which performed immediate analysis of collected samples and 2) an in situ proton transfer reaction mass spectrometer (PTR-MS) system operated by the University of Innsbruck. The sample protocols were quite different for the different methods. The GC systems sequentially collected and analyzed air samples each 15 minutes for VOC and each 3.5 minutes for PAN. Acetaldehyde, acetone & propanal, methanol, isoprene, methyl vinyl ketone (MVK)& methacrolein (MACR), toluene, and peroxyacetyl nitrate (PAN), were measured on a time shared basis for 2 to 10 seconds respectively, once each 30 seconds, by the PTR-MS system. The PTR-MS system is not able to distinguish between isobaric species, therefore acetone and propanal (MVK and MACR) values measured by NOAAs GC were added up prior to comparison with the respective PTR-MS values. For all species mentioned above the different measurement methods show good agreement.