Emerging therapeutic strategies for autoantibody-mediated diseases increasingly prioritise the selective reduction of pathogenic autoantibodies over global immune suppression, positioning autoantibodies as key mechanism of action (MoA) biomarkers in clinical trials. Autoimmune disorders such as systemic lupus erythematosus (SLE) and Sjögren’s disease (SjD) are characterised by the presence of multiple high-titre autoantibodies, necessitating robust multiplex quantification methods to enable precise and cost-effective monitoring of treatment-induced changes. This presentation introduces (semi)quantitative methodologies, including cut-point calibration using cohort-based reactivity thresholds, dilution curve analyses to determine autoantibody titres, alongside the integration of inline calibration using reference materials within the Luminex IntelliFlex DR system. The dual-reporter functionality of the IntelliFlex DR platform enables assay calibration by enabling concurrent detection of autoantibodies and internal calibration controls within a single measurement, thereby improving data accuracy and reproducibility. These advancements facilitate precise autoantibody quantification, supporting patient stratification based on distinct serological profiles and enabling the identification of disease subgroups with unique clinical phenotypes or differential treatment responses. The incorporation of internal calibration materials represents a significant advancement in multiplex quantification, reinforcing the utility of the IntelliFlex DR system for MoA biomarker analysis in clinical studies.