Alzheimer's disease (AD) is the most prevalent form of dementia in the elderly. Amyloid plaque formation through aggregation of the amyloid beta peptide derived from amyloid precursor protein (APP) is considered one of the hallmark processes leading to AD pathology; however, the precise role of APP in plaque formation and AD pathogenesis is yet to be determined. Using stable isotope labeling by amino acids in cell culture (SILAC) and MS, protein expression profiles of APP null, rat neuronal-like B103 cells were compared to B103695 cells that express the APP isoform, APP-695. A total of 2979 unique protein groups were identified among three biological replicates and significant protein expression changes were identified in a total of 102 nonredundant proteins. Some of the top biological functions associated with the differentially expressed proteins identified include cellular assembly, organization and morphology, cell cycle, lipid metabolism, protein folding, and PTMs. We report several novel biological pathways influenced by APP-695 expression in neuronal-like cells and provide additional framework for investigating altered molecular mechanisms associated with APP expression and processing and contribution to AD pathology.