Proton transfer reaction mass spectrometry (PTR-MS) is often employed to characterize gas-phase compounds in both indoor and outdoor environments. PTR-MS measurements are usually made without upstream chromatographic separation, so it can be challenging to differentiate between an ion of interest, its isomers, and fragmentation products from other species all detected at the same mass-to-charge ratio. These isomeric contributions and fragmentation interferences can confound the determination of accurate compound mixing ratios, the assignment of accurate chemical properties, and corresponding analyses of chemical fate. In this study, we deployed a gas chromatograph upstream of a PTR-MS to investigate contributions of isomers and fragmentation products for select indoor air-relevant chemicals. Measurements were made in a test house across a variety of indoor chemical sources, oxidants, and environmental conditions during the Chemical Assessment of Surfaces and Air (CASA) study. Observed confounding signals at each extracted ion chromatogram ranged from 0% (C2H6OH+, C8H24O4Si4H+, and C10H30O5Si5H+) to 98% (at C5H9+). For many ions, confounding signals varied between indoor conditions, and there were also differences between confounding signals across indoor vs. outdoor measurements. The relative contribution of sets of key structural isomers (e.g., C6-C8 carbonyls, xylenes, trimethylbenzenes, and monoterpenes) remained consistent throughout the measurement period despite changing indoor conditions. These relatively stable isomer distributions yielded stable chemical property assignments for these isomer sets. Taken together, these observations can inform future interpretations of PTR-MS signals measured in different indoor conditions without upstream chromatography.