Applications of Mass Spectrometry-Based Proteomics in Clinical Biochemistry: Recent Advances and Challenges

Background: Mass spectrometry-based proteomics has revolutionized clinical biochemistry by enabling high-throughput, sensitive, and quantitative analysis of complex protein mixtures in biological samples. Its applications span disease biomarker discovery, drug response profiling, and precision diagnostics. As the demand for personalized medicine grows, proteomic technologies offer unparalleled insights into dynamic protein expression, post-translational modifications, and protein–protein interactions that underlie health and disease. Methods and Results: This review highlights recent methodological advances and clinical applications of mass spectrometry (MS)-driven proteomics, with a focus on translational relevance. Innovations in sample preparation, label-free and isobaric quantification, and improvements in high-resolution MS instruments have expanded the depth and accuracy of protein identification. Targeted proteomic strategies such as multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) allow for precise quantification of clinically relevant proteins, including cardiac troponins, apolipoproteins, and cancer antigens. In oncology, MS-based proteomics has enabled molecular subtyping of tumors and monitoring of therapeutic resistance. In cardiovascular and neurodegenerative diseases, proteomic signatures are emerging as diagnostic and prognostic tools. Despite these advances, challenges remain in terms of standardization, reproducibility, data analysis, and clinical integration. Inter-individual variability, sample heterogeneity, and pre-analytical artifacts can compromise data interpretation. Moreover, regulatory pathways for clinical validation and adoption of proteomic assays are still evolving. Conclusion: Mass spectrometry-based proteomics represents a powerful tool for clinical biochemistry, bridging the gap between molecular discovery and personalized diagnostics. Continued technological refinement, coupled with robust bioinformatic frameworks and clinical validation, will be essential to fully realize the potential of proteomics in routine patient care and precision medicine.