This report is a feasibility study on the utility of gel-free proteomics in identifying peripheral biomarkers of brain injury. The study was performed in six pediatric patients admitted to the intensive care unit for severe traumatic brain injury (TBI). Serum samples collected at admission (less than 8 h after injury) were used for determining the levels of S100beta by enzyme-linked immunosorbent assay (ELISA) and for proteomics analyses. Serum samples were depleted of high abundant albumin and immunoglobulin, and were compared to a pooled reference from several healthy individuals. After labeling and separation on an ionic column, six different serum fractions were analyzed using Isotope-Coded Affinity Tag (ICAT), followed by tandem mass spectrometry (MS/MS) protein sequencing and identification. Ninety-five unique, differentially expressed proteins were identified, including several with a likely brain origin. Several proteins with pattern similarity to S100beta identified by hierarchical clustering could be considered for evaluation in a larger patient sample as potential peripheral markers of TBI.