Approximately 2 million traumatic brain injury (TBI) incidents occur annually in the United States, yet there are no specific therapeutic treatments. The absence of brain injury diagnostic endpoints was identified as a significant roadblock to TBI therapeutic development. To this end, our laboratory has studied mechanisms of cellular injury for biomarker discovery and possible therapeutic strategies. In this study, pooled naïve and injured cortical samples (48 hours post-injury; rat controlled cortical impact model) were processed and analyzed using a differential neuroproteomics platform. Protein separation was performed using combined cationic/anionic-exchange chromatography – polyacrylamide gel electrophoresis (CAX-PAGE). Differential proteins were then trypsinzed and analyzed with reversed-phase liquid chromatography tandem mass spectrometry (RPLC-MSMS) for protein identification and quantitative confirmation. The results included 59 differential protein components of which 21 decreased and 38 increased in abundance after TBI. Proteins with decreased abundance included collapsin response mediator protein-2 (CRMP-2), glyceraldehyde-3-phosphate dehydrogenase, microtubule associated proteins MAP-2A/2B, and hexokinase. Conversely, C-reactive protein, transferrin and breakdown products of CRMP-2, synaptotagmin and aII-spectrin were found elevated after TBI. Differential changes in the above-mentioned proteins were confirmed by quantitative immunoblotting. Results from this work provide insight into mechanisms of traumatic brain injury, and yield putative biochemical markers to potentially facilitate patient management by monitoring the severity, progression and treatment of injury.