Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation.

Autor: Nakayasu ES; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. ernesto.nakayasu@pnnl.gov., Gritsenko M; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA., Piehowski PD; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA., Gao Y; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA., Orton DJ; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA., Schepmoes AA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA., Fillmore TL; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA., Frohnert BI; Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA., Rewers M; Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA., Krischer JP; Morsani College of Medicine, University of South Florida, Tampa, FL, USA., Ansong C; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA., Suchy-Dicey AM; Elson S. Floyd College of Medicine, Washington State University, Seattle, WA, USA., Evans-Molina C; Center for Diabetes and Metabolic Diseases and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA., Qian WJ; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA., Webb-Robertson BM; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.; Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Metz TO; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.
Jazyk: angličtina
Zdroj: Nature protocols [Nat Protoc] 2021 Aug; Vol. 16 (8), pp. 3737-3760. Date of Electronic Publication: 2021 Jul 09.
DOI: 10.1038/s41596-021-00566-6
Abstrakt: Mass-spectrometry-based proteomic analysis is a powerful approach for discovering new disease biomarkers. However, certain critical steps of study design such as cohort selection, evaluation of statistical power, sample blinding and randomization, and sample/data quality control are often neglected or underappreciated during experimental design and execution. This tutorial discusses important steps for designing and implementing a liquid-chromatography-mass-spectrometry-based biomarker discovery study. We describe the rationale, considerations and possible failures in each step of such studies, including experimental design, sample collection and processing, and data collection. We also provide guidance for major steps of data processing and final statistical analysis for meaningful biological interpretations along with highlights of several successful biomarker studies. The provided guidelines from study design to implementation to data interpretation serve as a reference for improving rigor and reproducibility of biomarker development studies.
(© 2021. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)
Databáze: MEDLINE
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