Data-Independent Acquisition Mass Spectrometry To Quantify Protein Levels in FFPE Tumor Biopsies for Molecular Diagnostics

Overview

Journal J Proteome Res

Publisher American Chemical Society

Specialty Biochemistry

Date 2018 Nov 28

PMID 30481034

Citations 9

Authors

Yeoun Jin Kim

Steve M M Sweet

Jarrett D Egertson

Andrew J Sedgewick

Sunghee Woo

Wei-Li Liao

Gennifer E Merrihew

Brian C Searle

Charlie Vaske

Robert Heaton

Michael J MacCoss

Todd Hembrough

Affiliations

Soon will be listed here.

Abstract

Mass spectrometry-based protein quantitation is currently used to measure therapeutically relevant protein biomarkers in CAP/CLIA setting to predict likely responses of known therapies. Selected reaction monitoring (SRM) is the method of choice due to its outstanding analytical performance. However, data-independent acquisition (DIA) is now emerging as a proteome-scale clinical assay. We evaluated the ability of DIA to profile the patient-specific proteomes of sample-limited tumor biopsies and to quantify proteins of interest in a targeted fashion using formalin-fixed, paraffin-embedded (FFPE) tumor biopsies ( n = 12) selected from our clinical laboratory. DIA analysis on the tumor biopsies provided 3713 quantifiable proteins including actionable biomarkers currently in clinical use, successfully separated two gastric cancers from colorectal cancer specimen solely on the basis of global proteomic profiles, and identified subtype-specific proteins with prognostic or diagnostic value. We demonstrate the potential use of DIA-based quantitation to inform therapeutic decision-making using TUBB3, for which clinical cutoff expression levels have been established by SRM. Comparative analysis of DIA-based proteomic profiles and mRNA expression levels found positively and negatively correlated protein-gene pairs, a finding consistent with previously reported results from fresh-frozen tumor tissues.

Citing Articles

A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues.

Darville L, Lockhart J, Reddy S, Fang B, Izumi V, Boyle T Methods Mol Biol. 2024; 2823:193-223.

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Benefits of FAIMS to Improve the Proteome Coverage of Deteriorated and/or Cross-Linked TMT 10-Plex FFPE Tissue and Plasma-Derived Exosomes Samples.

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Antitumor activity of AZD0754, a dnTGFβRII-armored, STEAP2-targeted CAR-T cell therapy, in prostate cancer.

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Data-Independent Acquisition Mass Spectrometry Analysis of FFPE Rectal Cancer Samples Offers In-Depth Proteomics Characterization of the Response to Neoadjuvant Chemoradiotherapy.

Stanojevic A, Samiotaki M, Lygirou V, Marinkovic M, Nikolic V, Stojanovic-Rundic S Int J Mol Sci. 2023; 24(20).

PMID: 37895091 PMC: 10607861. DOI: 10.3390/ijms242015412.

Evaluation of Disposable Trap Column nanoLC-FAIMS-MS/MS for the Proteomic Analysis of FFPE Tissue.

Eckert S, Chang Y, Bayer F, The M, Kuhn P, Weichert W J Proteome Res. 2021; 20(12):5402-5411.

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