Longitudinal case-control study protocol for mapping caries susceptibility and could identify possible stable immunoproteomic markers in saliva

This document details the protocol for an unblinded, longitudinal case-control study designed to map caries susceptibility and potentially identify stable immunoproteomic markers in saliva. The study involves 46 systemically healthy adults (18-35 years old) and establishes distinct control and caries groups based on International Caries Detection and Assessment System (ICDAS) criteria. The protocol outlines the standardized collection of unstimulated and stimulated whole saliva at three time points (baseline, one and three months). The methodology covers personalized non-invasive/micro-invasive treatments for both groups, and invasive restorative procedures exclusively for the caries group. Detailed procedures for saliva sample processing are provided, including individual sample analysis using MALDI-TOF MS for microbial identification, and pooling strategies for subsequent nLC-MS/MS analysis, aimed at ensuring robust biomarker identification. Information regarding grant support (ANID grant #11190607), ethics approval (protocol #23-2019), and clinical study registration (ISRCTN64570618) is included, reaffirming the study's adherence to rigorous scientific and ethical standards.