Biomarker Discovery in Clinical Proteomics: Strategies for Exposing Low Abundant Proteins

Abstract

Disease specific proteins are highly valuable as clinical biomarkers, which can be used in early diagnosis, monitoring disease progressions and evaluating therapies. The identification and characterization of protein biomarkers in different physiological and pathological sources of interest under diverse milieu represent a key area of clinical proteomics. However, owing to the inherent complexities and the large dynamic ranges of proteins, there are many practical issues and challenges in discovering the low-abundance, disease-specific biomarkers from heterogeneous tissues and biofluids. Thus, an integrated approach for selective protein pre-fractionation, purification and separation, is necessary to detect low-abundant biomarkers in proteomics research. This review will summarize recent advancements in clinical sample preparation for removing high abundant proteins, as well as the improved two-dimensional gel electrophoresis-and mass spectrometry-based technologies for resolving low-abundant proteins. We will also elaborate the proteomic strategies for targeting protein sub-populations with special interests, such as high molecular weight protein complexes, membrane or its associated proteins, and organelle specific proteins etc. We will emphasize the use of these strategies to interrogate the current proteomic researches in clinical biomarker discovery.

Liquid‐phase‐based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids for in‐depth proteomics analysis

“…A typical example is the chlorotriazine dye Cibacron Blue (CB) that binds strongly to albumin 21–24. CB and its derivatives have been widely used to deplete albumin from serum samples 21, 25 and also in biomarkers discovery 26. The major drawback of this affinity media is the relatively high non‐specific interactions that usually result in removing many proteins in addition to albumin 8, 27.…”

“…CB binds to proteins that contain dinucleotide fold through specific affinity interaction as well as electrostatic, hydrophobic and hydrogen bonding interactions with the dye planar ring structure and the sulfate groups 11, 22, 28. For example, CB shows affinity toward nicotinamide adenine dinucleotide, flavine adenine dinucleotide and adenosine triphosphate binding site of proteins 25. Also, albumin was detected in pass‐through fraction when CB was used to deplete serum samples 27.…”