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Development Of A Highly Multiplexed SRM Assay For Biomarker Discovery In Formalin-Fixed Paraffin-Embedded Tissues.

Carine Steiner, P. Lescuyer, Jean-Christophe Tille, Paul Cutler, A. Ducret
Published 2019 · Medicine

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The search for novel and clinically relevant biomarkers still represents a major clinical challenge and mass-spectrometry-based technologies are essential tools to help in this process. In this application, we demonstrate how selected reaction monitoring (SRM) can be applied in a highly multiplexed way to analyze formalin-fixed paraffin-embedded (FFPE) tissues. Such an assay can be used to analyze numerous samples for narrowing down a list of potential biomarkers to the most relevant candidates. The use of FFPE tissues is of high relevance in this context as large sample collections linked with valuable clinical information are available in hospitals around the world. Here we describe in detail how we proceeded to develop such an assay for 200 proteins in breast tumor FFPE tissues. We cover the selection of suitable peptides, which are different in FFPE compared to fresh frozen tissues and show how we deliberately biased our assay toward proteins with a high probability of being measurable in human clinical samples.
This paper references
Cancer heterogeneity determined by functional proteomics.
A. Szasz (2017)
High HER2 protein levels correlate with increased survival in breast cancer patients treated with anti‐HER2 therapy
P. Nuciforo (2016)
Proteomic studies of formalin-fixed paraffin-embedded tissues
L. Giusti (2013)
Strategies to design clinical studies to identify predictive biomarkers in cancer research.
José Luis Pérez-Gracia (2017)
Shaping the future of biomarker research in breast cancer to ensure clinical relevance
M. Hinestrosa (2007)
Comparative Proteome Analysis Revealing an 11-Protein Signature for Aggressive Triple-Negative Breast Cancer
N. Q. Liu (2014)
Mass spectrometric analysis of formalin‐fixed paraffin‐embedded tissue: Unlocking the proteome within
B. Hood (2006)
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
T. Sørlie (2001)
The proteomics of formalin-fixed wax-embedded tissue.
David Cilia Vincenti (2013)
Molecular portraits of human breast tumours
C. Perou (2000)
Exploring the role of molecular biomarkers as a potential weapon against gastric cancer: A review of the literature.
M. Matboli (2016)
Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach*
S. Carr (2014)
Selected reaction monitoring for quantitative proteomics: a tutorial
V. Lange (2008)
Using iRT, a normalized retention time for more targeted measurement of peptides
Claudia Escher (2012)
Equivalence of Protein Inventories Obtained from Formalin-fixed Paraffin-embedded and Frozen Tissue in Multidimensional Liquid Chromatography-Tandem Mass Spectrometry Shotgun Proteomic Analysis*
Robert W. Sprung (2009)
Supervised risk predictor of breast cancer based on intrinsic subtypes.
J. Parker (2009)
Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded (FFPE) Breast Cancer Tissues*
Carine Steiner (2015)
A clinically relevant gene signature in triple negative and basal-like breast cancer
A. Rody (2011)
Extraction and Analysis of Diagnostically Useful Proteins from Formalin-fixed, Paraffin-embedded Tissue Sections
K. Ikeda (1998)
The Emergence of Precision Urologic Oncology: A Collaborative Review on Biomarker-driven Therapeutics.
C. Barbieri (2017)
Subtypes of breast cancer show preferential site of relapse.
M. Smid (2008)
Therapeutic targets in triple negative breast cancer
S. O’Toole (2013)
Peptide separation with immobilized pI strips is an attractive alternative to in‐gel protein digestion for proteome analysis
Nina C. Hubner (2008)
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
B. MacLean (2010)
Efficient method for the proteomic analysis of fixed and embedded tissues.
D. Palmer-Toy (2005)
Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry.
B. MacLean (2010)
Highly multiplexed targeted proteomics using precise control of peptide retention time
S. Gallien (2012)
Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides.
Alexander Scherl (2008)
Application of selected reaction monitoring for multiplex quantification of clinically validated biomarkers in formalin-fixed, paraffin-embedded tumor tissue.
Todd Hembrough (2013)
Scoring proteomes with proteotypic peptide probes
B. Kuster (2005)
Absolute Quantitation of Met Using Mass Spectrometry for Clinical Application: Assay Precision, Stability, and Correlation with MET Gene Amplification in FFPE Tumor Tissue
D. Catenacci (2014)

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