Atmospheric aerosols play an important role in the Earth's climate system. We present the analysis of atmospheric molecules/particles collected with a sampling system that can fly under regular weather balloons. The flights took place on 10 October 2022 from Reims and on 13 December 2022 from Orléans (France). The samples collected on activated carbon filters were analyzed by high-resolution mass spectrometry (Orbitrap Q-Exactive). Using Desorption electrospray ionization (DESI), we could derive hundreds of chemical formulas for organic species present in different layers from the troposphere to the stratosphere (up to 20 km). Measurements of O3, CO, and aerosol concentrations a few hours before these flights took place to contextualize the sampling.