Abdominal aortic aneurysm (AAA) is a significant health problem in Western countries. The diameter of AAA is a surrogate marker of its growth rate that reflects the magnitude of the degenerative process in the vascular wall, although most AAAs show discontinuous growth patterns and alternate periods of stability and nongrowth with periods of acute expansion and occasionally ruptures. Thus, the identification of biomarkers of AAA in plasma could aid in the diagnosis, prognosis, and therapy of AAA progression. However, owing to the complex composition of plasma, depletion methods must be applied before the analytical approaches for detecting low-abundant plasma protein components. In the present work, we describe a proteomic study on MARS 14-depleted plasma based on mass spectrometry (MS) which combines peptide labelling (isobaric tagging for relative and absolute quantification, iTRAQ) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). This quantitative approach revealed altered levels of several proteins related to the complement system in AAA patients.