Abstract. A method using thermal desorption sampling and analysis by proton transfer reaction mass spectrometry (PTR-MS) to measure long chain alkanes (C₁₂–C₁₈) and other larger organics associated with diesel engine exhaust emissions is described. Long chain alkanes undergo dissociative proton transfer reactions forming a series of fragment ions with formula C_nH_2n+1. The PTR-MS is insensitive to n-alkanes less than C₈ but displays an increasing sensitivity for larger alkanes. Fragment ion distribution and sensitivity is a function of drift conditions. At 80 Td the most abundant ion fragments from C₁₀ to C₁₆ n-alkanes were m/z 57, 71 and 85. The mass spectrum of gasoline and diesel fuel at 80 Td displayed ion group patterns that can be related to known fuel constituents, such as alkanes, alkylbenzenes and cycloalkanes, and other compound groups that are inferred from molecular weight distributions such as dihydronapthalenes and naphthenic monoaromatics. It is shown that thermal desorption sampling of gasoline and diesel engine exhausts at 80 Td allows for discrimination against volatile organic compounds, allowing for quantification of long chain alkanes from the abundance of C_nH_2n+1 fragment ions. The total abundance of long chain alkanes in diesel engine exhaust was measured to be similar to the total abundance of C₁–C₄ alkylbenzene compounds. The abundance patterns of compounds determined by thermal desorption sampling may allow for emission profiles to be developed to better quantify the relative contributions of diesel and gasoline exhaust emissions on organic compounds concentrations in urban air.