Abstract. During nucleation studies from pure isoprene oxidation in the CLOUD chamber at the European Organization for Nuclear Research (CERN) we observed unexpected ion signals at m∕z = 137.133 (C10H17+) and m∕z = 81.070 (C6H9+) with the recently developed proton-transfer-reaction time-of-flight (PTR3-TOF) mass spectrometer instrument. The mass-to-charge ratios of these ion signals typically correspond to protonated monoterpenes and their main fragment. We identified two origins of these signals: first secondary association reactions of protonated isoprene with isoprene within the PTR3-TOF reaction chamber and secondly [4+2] cycloaddition (Diels–Alder) of isoprene inside the gas bottle which presumably forms the favored monoterpenes limonene and sylvestrene, as known from literature. Under our PTR3-TOF conditions used in 2016 an amount (relative to isoprene) of 2 % is formed within the PTR3-TOF reaction chamber and 1 % is already present in the gas bottle. The presence of unwanted cycloaddition products in the CLOUD chamber impacts the nucleation studies by creating ozonolysis products as the corresponding monoterpenes and is responsible for the majority of the observed highly oxygenated organic molecules (HOMs), which in turn leads to a significant overestimation of both the nucleation rate and the growth rate. In order to study new particle formation (NPF) from pure isoprene oxidation under relevant atmospheric conditions, it is important to improve and assure the quality and purity of the precursor isoprene. This was successfully achieved by cryogenically trapping lower-volatility compounds such as monoterpenes before isoprene was introduced into the CLOUD chamber.