Transition from identity to bioactivity-guided proteomics for biomarker discovery with focus on the PF2D platform

Abstract

Proteomic strategies provide a valuable tool kit to identify proteins involved in diseases. With recent progress in MS technology, high throughput proteomics has accelerated protein identification for potential biomarkers. Numerous biomarker candidates have been identified in several diseases, and many are common among pathologies. An overall strategy that could complement and strengthen the search for biomarkers is combining protein identity with biological outcomes. This review describes an emerging framework of bridging bioactivity to protein identity, exploring the possibility that some biomarkers will have a mechanistic role in the disease process. A review of pulmonary, cardiovascular, and CNS biomarkers will be discussed to demonstrate the utility of combining bioactivity with identification as a means to not only find meaningful biomarkers, but also to uncover functional mediators of disease.

Keywords: Acute respiratory distress syndrome; Asthma; Atherosclerosis; Bioassay; Inflammation; Multiple sclerosis; PTMs; Proteoform; Validation assay.

Figure 1.

From identity to bioactivity-guided proteomics. (A) Identity-guided proteomics focuses on the most efficient and reliable way to identify proteins and peptides from a complex sample. Priority is given to efficient protein extraction, sometimes after several enrichment steps, and processing through a MS-coupled system for identification. Validation of the protein(s) of interest occurs at the final stage of the entire strategy. Identity-guided proteomics can theoretically identify and quantify intact or fragmented proteins from any kind of sample, but often suffers from low success rate in identifying new biomarkers due to incomplete validation. (B) Bioactivity-guided proteomics focuses on the most biologicaly relevant protein(s) from a complex sample. Emphasis is given to sequential validation using bioassay(s), before processing through MS-coupled system and identification. It requires intact proteins or at least biologically active ones and the development of reliable and sensitive bioassay(s). Additional validation of the protein of interest can be performed at the end of the strategy. The sequential validation performed during bioactivity-guided proteomics should improve the success rate of biomarkers usable in the clinic.