How shall we use the proteomics toolbox for biomarker discovery?

TL;DR

This paper analyzes challenges in proteomics-based biomarker discovery and proposes alternative strategies to improve success rates, focusing on sample source selection and protein targeting methods.

Contribution

It provides a critical analysis of current proteomics strategies and suggests new approaches to overcome limitations in biomarker discovery.

Findings

Limited success in clinical biomarker discovery due to methodological issues

Switching to cell and tissue samples can improve biomarker identification

Highly selective protein strategies may enhance biomarker detection

Abstract

Biomarker discovery for clinical purposes is one of the major areas in which proteomics is used. However, despite considerable effort, the successes have been relatively scarce. In this perspective paper, we try to highlight and analyze the main causes for this limited success, and to suggest alternate strategies, which will avoid them, without eluding the foreseeable weak points of these strategies. Two major strategies are analyzed, namely, the switch from body fluids to cell and tissues for the initial biomarker discovery step or, if body fluids must be analyzed, the implementation of highly selective protein selection strategies.