CE, interfaced off-line to MALDI-TOF/TOF MS, was for the first time used to quantitatively monitor the protein content in complex biological and clinical samples with iTRAQ (TM) labeling. The usefulness and advantage of iTRAQ (TM) labeling, in combination, with CE MALDI-TOF/TOF MS is demonstrated on mixtures of protein standards and by a case study on human ventricular cerebrospinal fluid samples collected from a patient with traumatic brain injury during patient recovery. Mixtures of five standard proteins were initially analyzed to optimize the experimental conditions for the CE MALDI-MS and MS/MS analysis. The interactions of proteins and peptides with the capillary inner wall during CE separation were minimized using PolyE-323 modified capillaries. The analysis of the ventricular cerebrospinal fluid samples yielded 43 significantly (p < 0.05 MudPIT scoring) identified proteins that could be quantitatively monitored over time. The identified changes in protein levels for several of these proteins are well in line with the reports from previous studies on protein patterns that could be related to the post-traumatic processes of traumatic brain injury. This study shows that the presented approach, combining isobaric tags with CE MALDI-TOF/TOF MS, is a useful choice for quantitative proteomic analysis.