Abstract
Nowadays, significant difficulties remain in the diagnosis and/or prognosis of many diseases, leading to an unsatisfactory patient management and a counterproductive increase in time and costs. It is therefore crucial to bridge the gap between basic and applied research by complying with clinical requirements, notably from the design stage of the experimental workflow. In this chapter we provide key suggestions for selecting appropriate biological samples and reducing pre-analytical and analytical variabilities to improve the discovery of clinically relevant protein biomarkers.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Fuzery AK, Levin J, Chan MM et al (2013) Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges. Clin Proteomics 10(1):13. https://doi.org/10.1186/1559-0275-10-13
Pepe MS, Li CI, Feng Z (2015) Improving the quality of biomarker discovery research: the right samples and enough of them. Cancer Epidemiol Biomark Prev 24(6):944–950. https://doi.org/10.1158/1055-9965.EPI-14-1227
Farina A (2014) Proximal fluid proteomics for the discovery of digestive cancer biomarkers. Biochim Biophys Acta 1844(5):988–1002. https://doi.org/10.1016/j.bbapap.2013.10.011
Dakappagari N, Zhang H, Stephen L et al (2017) Recommendations for clinical biomarker specimen preservation and stability assessments. Bioanalysis 9(8):643–653. https://doi.org/10.4155/bio-2017-0009
Percy AJ, Parker CE, Borchers CH (2013) Pre-analytical and analytical variability in absolute quantitative MRM-based plasma proteomic studies. Bioanalysis 5(22):2837–2856. https://doi.org/10.4155/bio.13.245
Baek R, Sondergaard EKL, Varming K et al (2016) The impact of various preanalytical treatments on the phenotype of small extracellular vesicles in blood analyzed by protein microarray. J Immunol Methods 438:11–20. https://doi.org/10.1016/j.jim.2016.08.007
Yuana Y, Bertina RM, Osanto S (2011) Pre-analytical and analytical issues in the analysis of blood microparticles. Thromb Haemost 105(3):396–408. https://doi.org/10.1160/Th10-09-0595
Jambunathan K, Galande AK (2014) Sample collection in clinical proteomics-Proteolytic activity profile of serum and plasma. Proteomics Clin Appl 8(5–6):299–307. https://doi.org/10.1002/prca.201300037
Chutipongtanate S, Chatchen S, Svasti J (2017) Plasma prefractionation methods for proteomic analysis and perspectives in clinical applications. Proteomics Clin Appl 11(7–8). https://doi.org/10.1002/prca.201600135
Ivanov AR, Lazarev A (eds) (2011) Sample preparation in biological mass spectrometry. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0828-0
Wisniewski JR, Wegler C, Artursson P (2016) Subcellular fractionation of human liver reveals limits in global proteomic quantification from isolated fractions. Anal Biochem 509:82–88. https://doi.org/10.1016/j.ab.2016.06.006
Lukic N, Visentin R, Delhaye M et al (2014) An integrated approach for comparative proteomic analysis of human bile reveals overexpressed cancer-associated proteins in malignant biliary stenosis. Biochim Biophys Acta 1844(5):1026–1033. https://doi.org/10.1016/j.bbapap.2013.06.023
Farina A, Dumonceau JM, Delhaye M et al (2011) A step further in the analysis of human bile proteome. J Proteome Res 10(4):2047–2063. https://doi.org/10.1021/pr200011b
Choksawangkarn W, Edwards N, Wang Y et al (2012) Comparative study of workflows optimized for in-gel, in-solution, and on-filter proteolysis in the analysis of plasma membrane proteins. J Proteome Res 11(5):3030–3034. https://doi.org/10.1021/pr300188b
Acknowledgment
The author sincerely thanks all the coworkers who, over the years, have substantially contributed in the acquisition of the know-how required for the development of the present protocols, notably: Dr. Yohann Couté (Exploring the Dynamics of Proteomes laboratory at the CEA, Grenoble, France) for the methodological advices about each phase of protein identification and quantitation; Dr. Valeria Severino (Digestive Cancers Biomarkers Group of the Medicine Faculty at the Geneva University, Geneva, Switzerland) for the improvement of protein sub-fractionation protocols; The Proteomic Core Facility (Medicine Faculty at the Geneva University, Geneva, Switzerland) for the adaptation of peptide cleanup methods; Dr. Pierre Lescuyer, (Department of Genetic, Laboratory and Pathology Medicine at the Geneva University Hospitals, Geneva, Switzerland) for crucial knowledge in clinical laboratory requirements; Dr. Jean-Marc Dumonceau (Gedyt Center, Argentina, Buenos Aires) for essential expertise in sample inclusion and collection; Prof. Jean-Louis Frossard (Gastroenterology and Hepatology Service at the Geneva University Hospitals, Geneva, Switzerland) for strong competences in digestive pathologies, constructive criticisms, and continuous help and support; all the trainee students involved in the analyses that allowed assembling and validating the protocols.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Farina, A. (2019). Pre-fractionation of Noncirculating Biological Fluids to Improve Discovery of Clinically Relevant Protein Biomarkers. In: Brun, V., Couté, Y. (eds) Proteomics for Biomarker Discovery. Methods in Molecular Biology, vol 1959. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9164-8_2
Download citation
DOI: https://doi.org/10.1007/978-1-4939-9164-8_2
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-9163-1
Online ISBN: 978-1-4939-9164-8
eBook Packages: Springer Protocols