Proteomic Biomarker Discovery: Review of the Science and Its Challenges with Clinical Samples

Proteomics is a science that facilitates global analysis of protein expression, molecular interactions and functional states of protein in a cell, organ or organism under consideration. Protein at the molecular level represents the biological endpoint and therefore more suitable to assess cellular responses. Proteins biomarkers are routinely used in cancers for different purposes such as diagnosis, screening and predicting therapy responses. Proteomic science utilise both cell line models and clinical samples to make novel discoveries. Compared to cell lines, clinical samples provide more accurate representation of the tumour micro-environment, explore and identify stromal molecular targets. However, using clinical samples for biomarker discovery has its own challenges. In this review, we aim to provide clinicians an overview of the proteomic biomarker discovery pathway, examine the use of different clinical samples in proteomic research and highlight the limitations and challenges of using clinical samples with proteomic methods.