A Review of Neuroproteomics in Neurological Disorders: The Use of Machine Learning and Deep Learning

Proteomics has emerged as a powerful tool for advancing our understanding of brain disorders by enabling large-scale characterization of protein expression, post-translational modifications, and interaction networks. Neurological conditions are often characterized by complex and dynamic molecular changes that are not fully captured by traditional diagnostic approaches. Proteomic technologies, particularly mass spectrometry-based and affinity-based methods, offer the ability to identify disease-specific protein signatures and elucidate underlying pathophysiological mechanisms, including neurodegeneration, neurodevelopment and neuroinflammation and alterations happening to the extracellular matrix and body fluid homeostasis. In recent years, artificial intelligence has emerged as a powerful tool to proteomics, enabling improved analysis of complex biological datasets. This integration has significantly enhanced the discovery of biomarkers for early diagnosis, disease stratification, and monitoring of therapeutic responses. Thus, cerebrospinal fluid and blood-based proteomic analyses have revealed promising candidates for neurological diseases. This review summarizes current advances in proteomics across a range of brain disorders, highlighting key molecular pathways, biomarker discovery efforts, and evolving clinical applications. Furthermore, it outlines future directions, including the application of machine learning for improved biomarker identification and precision medicine.