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Study on Tissue Homogenization Buffer Composition for Brain Mass Spectrometry-Based Proteomics

ORCID
0000-0002-1798-4021
Affiliation
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
Karpiński, Adam Aleksander;
Affiliation
Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
Torres Elguera, Julio Cesar;
ORCID
0000-0002-6662-7039
Affiliation
Institute for Biochemistry and Molecular Biology (IBMB), Medical Faculty, University of Bonn, Nußallee 11, 53115 Bonn, Germany
Sanner, Anne;
Affiliation
Lukasiewicz Research Network—PORT Polish Center for Technology Development, Stablowicka 147, 54-066 Wroclaw, Poland
Konopka, Witold;
Affiliation
Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland
Kaczmarek, Leszek;
ORCID
0000-0001-6788-6641
Affiliation
Institute for Biochemistry and Molecular Biology (IBMB), Medical Faculty, University of Bonn, Nußallee 11, 53115 Bonn, Germany
Winter, Dominic;
Affiliation
Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
Konopka, Anna;
Affiliation
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
Bulska, Ewa

Mass spectrometry-based proteomics aims to study the proteome both qualitatively and quantitatively. A key step in proteomic analysis is sample preparation, which is crucial for reliable results. We investigated the effect of the composition of the homogenization buffer used to extract proteins from brain tissue on the yield of protein extraction and the number and type of extracted proteins. Three different types of buffers were compared—detergent-based buffer (DB), chaotropic agent-based buffer (CAB) and buffer without detergent and chaotropic agent (DFB). Based on label-free quantitative protein analysis, detergent buffer was identified as the most suitable for global proteomic profiling of brain tissue. It allows the most efficient extraction of membrane proteins, synaptic and synaptic membrane proteins along with ribosomal, mitochondrial and myelin sheath proteins, which are of particular interest in the field of neurodegenerative disorders research.

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