JIOMICS

JIOMICS | VOL 5 | ISSUE 2 | DECEMBER 2015 | 1-62
JOURNAL OF INTEGRATED OMICS
Journal of Integrated Omics
A METHODOLOGICAL JOURNAL
HTTP://WWW.JIOMICS.COM
Special Issue: Proceeding Abstracts of the 4 th International Congress on Analytical Proteomics (ICAP 2015)
A quest for innovative and robust biomarkers using MS-based proteomics
L. Dayon*, A. Núñez Galindo, John Corthésy, S. Oller Moreno, O. Cominetti, M. Kussmann
Molecular Biomarkers Core, Nestlé Institute of Health Sciences, Lausanne, Switzerland. *Corresponding author: loic.dayon@rd.nestle.com
Available Online: 31 December 2015
Abstract
Purpose: The identification of novel biomarkers with proven clinical utility relies on a complex process composed of discovery, qualification,
verification, and validation steps. Proteomic biomarker discovery has provided numerous candidates but only few of those have reached
the validation stage and even less are used in today’s routine clinical practice. Mass spectrometry (MS)-based proteomics is powerful enough to
comprehensively characterize biological and clinical samples but offers limited sample throughput, mainly due to complex sample preparation
upstream of MS. Proteomic biomarker discovery studies are therefore often performed with a too small number of samples, compromising
study design. We have developed dedicated highly-automated workflows to facilitate, accelerate, and improve molecular phenotyping and
translation of clinical proteomic discovery findings in human body fluids such as plasma and cerebrospinal fluid.
Experimental description: A highly automated MS-based proteomic discovery approach that comprises immuno-affinity depletion of abundant
plasma proteins, buffer exchange, reduction/alkylation, tryptic digestion, isobaric labeling, sample purification and reversed-phase liquid
chromatography tandem MS analysis was developed, characterized [1] and finally used to analyze cohorts of patients, ranging from 100 to
1’000 individuals [2].
Results: Analytical figures of merit, e.g., precision and trueness, of our approach demonstrated increased robustness compared to to-date
published manual or less automated workflows while ensuring sufficient throughput for large-scale studies. Application to clinical biomarker
research programs in the fields of metabolic and brain health provided protein biomarker models for stratification of subjects and prediction of
relevant clinical readouts.
Conclusions: Our results revealed that the analysis of large number of samples for biomarker discovery in clinical research using today’s
MS-based shotgun proteomics technology has become feasible. The analytical and biological consistency of our results regarding technical
validation but also clinical research demonstrated the value of our approach.
Keywords: Biomarker; Body fluid; Blood; Clinical proteomics; Mass spectrometry; Obesity; Alzheimer’s disease.
References:
[1] Dayon, L.; Núñez Galindo, A.; Corthésy, J.; Cominetti, O.; Kussmann, M., Comprehensive and scalable highly automated MS-based proteomic
workflow for clinical biomarker discovery in human plasma. J. Proteome Res. 2014, 13, (8), 3837-3845.
[2] Cominetti, O.; Núñez Galindo, A.; Corthésy, J.; Oller Moreno, S.; Irincheeva, I.; Valsesia, A.; Astrup, A.; Saris, W.H.M.; Hager, J.; Kussmann,
M.; Dayon L., Proteomic Biomarker Discovery in 1'000 Human Plasma Samples with Mass Spectrometry: Vision or Reality?. Submitted.
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