Biogenic volatile organic compounds (BVOCs) are major precursors of secondary organic aerosol (SOA) and new particle formation (NPF), and therefore play an important role in the climate system, altering the abundance of cloud condensation nuclei (CCN). Ozonolysis of the most atmospherically abundant monoterpene, α-pinene, generates RO₂ radicals which undergo autoxidation, resulting in the formation of oxygenated organic molecules (OOMs) with low volatility, an essential step in nucleation and early particle growth. However, quantitative interpretation of widely used mass spectrometric OOM measurements remains limited by reagent-ion selectivity and the lack of authentic monomeric standards, an issue that is particularly important for hydroperoxides and peroxy acids, which constitute a significant fraction of autoxidation products. Here, we synthesize two α-pinene-derived monomeric OOM standards, peroxy norpinonic acid (PNPA; C₉H₁₄O₄) and peroxy pinonic acid (PPA; C₁₀H₁₆O₄), and confirm their structures by ¹H and ¹³C NMR. We then evaluate their detectability using a MION-Orbitrap operated with nitrate (NO₃^−) and uronium (CH₅N₂O⁺) chemical ionization and compare these gas-phase schemes to heated electrospray ionization (H-ESI). NMR shows that freshly prepared standards are dominated by peroxy acids and contain only a fraction of the corresponding carboxylic acids, whereas Orbitrap measurements consistently yield substantially lower peroxy-to-carboxylic-acid ratios. These ratios vary strongly across ionization modes, with greater apparent peroxy acid loss under harder (de)protonation and improved, though still incomplete, preservation under softer nitrate and uronium adduct formation, indicating that the decomposition originates during ionization. Notably, uronium provides significantly higher sensitivity for these moderately oxygenated compounds, complementing nitrate’s strong selectivity toward highly oxygenated molecules (HOMs). Together, our results suggest that peroxy acids formed via α-pinene autoxidation may be systematically under-quantified by commonly used mass spectrometric approaches, with implications for O:C assignments, volatility-basis-set derivations, and inferred atmospheric process rates of nucleation and early particle growth.