The Portland Alcohol Research Center (PARC) was established to investigate the genetic basis of alcohol dependence. One line of inquiry utilizes mouse strains that are widely divergent in alcohol‐related behaviors. Decades of genetics research comparing mouse strains has identified many regions of the genome associated with such quantitative traits. These regions are called Quantitative Trait Loci (QTLs). Microarrays have been used to identify which genes within the QTLs are differentially expressed and are therefore potentially causal; however, genetic variants that affect probe hybridization lead to many false conclusions. Here, we used quantitative proteomics to compare brain striata between two mouse strains for which abundant QTL and transcriptomic data is available. The primary aims of this research were to (1) identify differentially expressed proteins that lie within QTLs and are therefore candidate causal proteins, (2) determine if genetic variants also lead to spurious results in quantitative proteomics, and (3) compare transcriptomic and proteomic datasets to determine their agreement.