Study on Tissue Homogenization Buffer Composition for Brain Mass Spectrometry-Based Proteomics
Adam Aleksander Karpiński,
Julio Cesar Torres Elguera,
Anne Sanner,
Witold Konopka,
Leszek Kaczmarek,
Dominic Winter,
Anna Konopka,
Ewa Bulska
Affiliations
Adam Aleksander Karpiński
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
Julio Cesar Torres Elguera
Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
Anne Sanner
Institute for Biochemistry and Molecular Biology (IBMB), Medical Faculty, University of Bonn, Nußallee 11, 53115 Bonn, Germany
Witold Konopka
Lukasiewicz Research Network—PORT Polish Center for Technology Development, Stablowicka 147, 54-066 Wroclaw, Poland
Leszek Kaczmarek
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
Dominic Winter
Institute for Biochemistry and Molecular Biology (IBMB), Medical Faculty, University of Bonn, Nußallee 11, 53115 Bonn, Germany
Anna Konopka
Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
Ewa Bulska
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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.
