Secondary organic aerosol (SOA) is a key uncertainty in quantifying the impact of humans on Earth's climate. SOA is a complex mixture of oxidized organic species, and a fundamental hurdle in determining its composition is the lack of authentic standards for comparison and quantification. Organic synthesis can be used to produce pure standards, but is limited to compounds for which there is a degree of confidence in the proposed structure and can be expensive and time-consuming. In this study, a flow reactor was developed to form SOA in sufficient quantities to be collected and pure compounds subsequently isolated from the mixture using semipreparative high performance liquid chromatography. The purity and yield of each isolated compound were obtained using proton nuclear magnetic resonance ((1)H NMR), whereas molecular formulas were confirmed by high resolution Fourier transform ion cyclotron mass spectrometry (FTICR-MS). The effectiveness of the methodology has been evaluated here by using α-pinene as the precursor because it is the monoterpene with the most well characterized SOA chemistry. Eleven individual α-pinene SOA compounds were produced from α-pinene oxidation experiments and used for quantitative analysis of SOA formed during chamber experiments carried out close to ambient conditions. These compounds represented 25% of the total SOA mass, a significant improvement in mass balance compared to previous studies. This relatively simple approach may be extended to produce other SOA components not available commercially to improve quantification of aerosol sources.