Technical report: The clinically useful selection of proteins protocol: An approach to identify clinically useful proteins for validation.

Clinical proteomics studies aiming to develop markers of clinical outcome or disease typically involve distinct discovery and validation stages, neither of which focus on the clinical applicability of the candidate markers studied. Our Clinically Useful Selection of Proteins (CUSP) protocol proposes a rational approach, with statistical and non-statistical components, to identify proteins for the validation phase of studies that could be most effective markers of disease or clinical outcome. Additionally, this protocol considers commercially available analysis methods for each selected protein to ensure that use of this prospective marker is easily translated into clinical practice. SIGNIFICANCE: When developing proteomic markers of clinical outcomes, there is currently no consideration at the validation stage of how to implement such markers into a clinical setting. This has been identified by several studies as a limitation to the progression of research findings from proteomics studies. When integrated into a proteomic workflow, the CUSP protocol allows for a strategically designed validation study that improves researchers' abilities to translate research findings from discovery-based proteomics into clinical practice.

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