Implementing proteomics-based solutions has emerged as a potentially highly powerful and transformative approach in enhancing patient management by streamlining clinical decision-making and accelerating drug development. Specific changes in proteins are generally responsible for onset and progression of disease. This understanding serves as a foundation for identifying biomarkers, discovering drug targets, and developing novel therapeutics. Despite substantial progress, several challenges and gaps persist. These include among others technical limitations, regulatory hurdles, legal, ethics and data protection issues. Addressing these obstacles necessitates a multifaceted approach involving critical evaluation, cross-disciplinary collaboration, and the inclusion of diverse stakeholder perspectives. Such a comprehensive strategy appears essential for advancing proteomics from research to implementation, ultimately benefiting patients. To this end, the PROTEOMICS journal is launching a special section dedicated to clinical proteomics. This initiative aims to highlight the critical aspects of (prote)omics-guided biomarker and drug development, address existing challenges, and propose potential solutions for implementation. By fostering collaboration among scientists, clinicians, patients, regulators, insurance companies, pharmaceutical companies, and funding agencies, we hope to spark discussions that pave the way for adopting proteomics-based approaches to improve patient outcomes.

The clinical proteomics field has seen enormous growth in the past 20 years, with over 40000 scientific manuscripts published. At the same time, actual clinical application of the reported findings is obviously scarce. In this manuscript we discuss the key issues that may be responsible for this apparent lack of success, which cannot be measured by the numbers of publications, but by the impact on patient management and treatment. We proceed with suggestions for potential solutions, which include keeping a strict focus on potential patient benefit. We hope this manuscript can help shaping the field, so it can in fact deliver on its realistic promise, to bring significant improvement in management and care to patients.

Extracellular matrix (ECM) proteins, including collagens, ECM glycoproteins, and proteoglycans, are critical components of tissue structure and function. In addition to the core matrisome, there are matrisome-associated proteins that balance ECM production and degradation. The identification and quantification of ECM proteins using mass spectrometry is often hindered by their low abundance and their tendency to aggregate, forming insoluble macromolecules in aqueous solutions. In this study, we aimed to investigate the effectiveness of a decellularization strategy that combined freeze-thaw cycles and sodium dodecyl sulphate treatment, in identifying and quantifying ECM proteins in mouse kidney using mass spectrometry. This decellularization strategy preserved 95% of the Core matrisome proteins detected in non-decellularized kidney and revealed additional once. Decellularization also led to an increase in the abundance of 96% of the core matrisome ECM proteins by an average of 59 times due to the successful removal of cellular and matrisome-associated proteins. However, the enrichment varied greatly among ECM proteins, resulting in a misrepresentation of the native ECM protein composition of the kidney. This should be brought to the attention of the matrisome research community, as it highlights the need for caution when interpreting proteomic data obtained following a decellularization procedure.

Type II diabetes mellitus (T2DM) accounts for approximately 90% of all diabetes mellitus cases in the world. Glucagon-like peptide-1 receptor (GLP-1R) agonists have established an increased capability to target directly or indirectly six core defects associated with T2DM, while, the underlying molecular mechanisms of these pharmacological effects are not fully known. This exploratory study was conducted to analyze the effect of treatment with GLP-1R agonists on urinary peptidome of T2DM patients. Urine samples of thirty-two T2DM patients from the PROVALID study (A Prospective Cohort Study in Patients with T2DM for Validation of Biomarkers) collected at pre- and post-treatment with GLP-1R agonist drugs were analyzed by CE-MS. In total, 70 urinary peptides were significantly affected by GLP-1R agonist treatment; generating from 26 different proteins. The downregulation of MMP proteases, based on the concordant downregulation of urinary collagen peptides was highlighted. Treatment also resulted in downregulation of peptides from SERPINA1, APOC3, CD99, CPSF6, CRNN, SERPINA6, HBA2, MB, VGF, PIGR and TTR, many of which were previously found to be associated with increased insulin resistance and inflammation. The findings indicate potential molecular mechanisms of GLP-1R agonists in the context of management of T2DM and prevention or delaying the progression of its associated diseases.