Interspecific hybrid grape varieties (Vitis spp.) are cultivated by grape breeding initiatives due to wild Vitis’ resistance to abiotic and biotic stress. However, these cultivars suffer from multiple flavor challenges, such as off-aromas and excessive sourness in the final wine product. When profiling volatiles in hybrid mapping populations, we performed headspace solid-phase microextraction (HS-SPME) coupled to gas chromatography–mass spectrometry (GC-MS), and quantitated select off-odorants using matched, isotopically labeled isotopologues. Seeking to move toward a less targeted approach, we tested the assumption that any relative changes in matrix effects among individuals would be similar for all compounds, i.e., matrix effects do not show Compound × Individual interactions. Individuals from two plant populations were analyzed: an interspecific grape (Vitis spp.) mapping population (n = 140) and a tomato (Solanum spp.) recombinant inbred line (RIL) population (n = 148). Individual plants from the two populations were spiked with a cocktail of internal standards (n = 6, 9, respectively) prior to HS-SPME-GC-MS. Variation in the relative responses of internal standards indicated that Compound × Individual interactions exist, but were different between the two populations. For the grape population, relative responses among pairs of internal standards varied considerably among individuals, with a maximum of 249% relative standard deviation (RSD) for the pair of [U13C]hexanal and [U13C]hexanol. However, in the tomato population, relative responses of internal standard pairs varied much less, with pairwise RSDs ranging from 8% to 56%. This post-hoc methodology can be applied to evaluate the suitability of using surrogate standards for HS-SPME-GC-MS studies in other plant populations. A related project evaluated the development of malate in wild Vitis spp. during berry maturation. Over a two-year study, samples from V. riparia, V. cinerea, V. vinifera, and hybrid spp. were taken at multiple time points. In contrast to the well-known biphasic behavior of malate in vinifera, we observed a range of behaviors in wild species. On average, riparia accessions had malate per berry comparable to vinifera just prior to veraison, but degraded malate at a slower rate. Cinerea accessions had significantly lower malate prior to veraison than all other groups, but showed a post-veraison increase in malate. Post-veraison malate degradation rates of interspecific hybrids were intermediate to vinifera and riparia. Variation in post-veraison malate behavior could be related to diminished malate degradation in the pulp of wild Vitis spp. Our results indicate that studies of malate behavior in Vitis spp. and their hybrids should include both pre- and post-veraison time points.