Comparison of extraction methods for the comprehensive analysis of mouse brain proteome using shotgun-based mass spectrometry

Journal of Proteome Research
Ganna ShevchenkoJonas Bergquist

Abstract

This study compares 16 different extraction methods for the comprehensive extraction of mouse brain proteome in combination with "shotgun"-based mass spectrometry (MS). Membrane proteins (MPs) are responsible for a large part of the regulatory functions of the cell and are therefore of great interest to extract and analyze. Sixteen protein extraction protocols were evaluated in regards to protein yield and number of identified proteins with emphasis on MPs. The extracted proteins were delipidated, on-filter digested, and analyzed by reversed phase nanoliquid chromatography (RP-nanoLC) in combination with electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using a 7 T hybrid LTQ-FT mass spectrometer. Detergent-based lysis buffers showed higher efficiencies and yields in the extraction of proteins from the brain tissue compared to solubilization with organic solvents or organic acids. The detergent octyl-β-D-glucopyranoside gave the highest number of identified proteins (541) as well as numbers and percentages of identified MPs (29%). Detergent-based protocols are the best sample preparation tools for central nervous system (CNS) tissue and can readily be applied to screen for candidate biomarkers of neurological disea...Continue Reading

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Citations

Feb 14, 2013·Analytical Chemistry·Glenn A HarrisRichard M Caprioli
May 14, 2014·Expert Review of Molecular Diagnostics·George Mermelekas, Jerome Zoidakis
May 23, 2014·Journal of Proteomics·Kristin ElfKonstantin Artemenko
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Dec 14, 2017·BioTechniques·Kyle A BurgessAlberto Saiani
Oct 17, 2018·Journal of Neurochemistry·Ubadah SabbaghMichael A Fox
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Jul 1, 2014·The Analyst·Nina Bergman, Jonas Bergquist
Aug 16, 2019·PloS One·Benjamin Yii Chung Lau, Abrizah Othman
Nov 3, 2017·Neuron·Fabian Hosp, Matthias Mann

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