Integrated Proteomic Profiling of Gingival Crevicular Fluid and Tooth Surface-Collected Material Reveals Potential Inflammatory Signatures in Periodontitis Post-Therapy: An Exploratory Study

Background: Characterizing the molecular microenvironment of periodontitis (PD) is essential for identifying non-invasive biomarkers. This study compared the total protein content and qualitative protein profiles of gingival crevicular fluid (GCF) and tooth surface-collected material (TSCM) from healthy individuals and patients with PD before and after non-surgical periodontal therapy (NSPT). Methods: GCF and TSCM samples were collected at baseline (T0) and 3 months after NSPT (T1) from 20 systemically healthy subjects: 10 healthy controls and 10 patients with stage III–IV PD. The control and PD groups were not age- and gender-matched. In PD patients, GCF was sampled from healthy and pathological sites. Total protein concentration was quantitatively assessed by the Bradford assay, while proteins were qualitatively characterized in differential SDS-PAGE fractions by LC-MS/MS analysis of pooled samples. Results: NSPT significantly improved clinical periodontal parameters (p < 0.05). Total protein concentration was higher in PD patients than in controls (p < 0.05). Baseline analysis revealed differential protein patterns, with identification of acute-phase and immune-related proteins in pathological GCF and TSCM samples. These alterations were markedly reduced after NSPT, accompanied by the identification of proteins associated with tissue protection and homeostasis. Healthy sites in PD patients also displayed distinct protein profiles, suggesting the presence of a subclinical inflammatory state. Conclusions: Combined proteomic analysis of GCF and TSCM provided exploratory evidence of molecular changes associated with PD and response to therapy. Given the small, non-matched groups and pooled-sample design, further validation is required to assess their potential applicability for the future management of PD.