An attractive method for osteoarthritis (OA) staging is the measurement of biochemical markers in biological fluids, which could reflect dynamic and quantitative changes in joint remodeling and therefore disease progression. Proteome analysis has been recognized as one of the most effective tools to explore biomarkers as it can furnish a wealth of information in both diagnosis and prognosis of diseases. We have recently described an innovative tool for peptidome and lipidome profiling of fluids based on mesoporous aluminosilicate (MPAS) and Matrix-Assisted Laser Desorption/Ionization time-of-flight Mass Spectrometry (MALDI-TOF MS). The aim of this study was to analyze peptide profiles of human synovial fluid in patients with different grade of OA using MALDI-TOF-MS technique in order to identify potential markers of disease progression. Twenty-five patients older than 50 years and affected by primary knee OA diagnosed according to clinical and radiological criteria were enrolled. For each patient a synovial fluid sample was aspirated from the affected knee and analyzed using MALDI-TOF-MS technique. A statistically significant difference in the normalized area of two peaks (m/z=1865 and m/z=2021) was detected among different stages of OA. The 2 peaks were identified as Complement C3 peptide fragments: C3f and C3f Des-Arg. The expression levels of these two peptides (m/z=1865 and 2021) decreased with the progression of OA degrees severity (ρs=-0.434, p=0.03, and ρs=-0.532, p=0.006, respectively). This marker may be a useful tool for assessing the severity of knee OA and it may be a novel target for drug discovery, specifically for the development of disease modifying OA drugs. However further studies are required to clarify the role of C3f in OA pathogenesis.