biostudies-literatureHirano STakeda Science FoundationMinistry of Education, Culture, Sports, Science and TechnologyJapan Society for the Promotion of Science383https://www.ebi.ac.uk/biostudies/studies/S-EPMC8962430biostudies-literatureUnknown10(2)The purpose of this study was to develop a method to comprehensively determine the localization of apical and basolateral membrane proteins, using a combination of apical/basolateral membrane separation and accurate SWATH (<b>S</b>equential <b>W</b>indow <b>A</b>cquisition of all <b>TH</b>eoretical fragment ion spectra) proteomics. The SWATH analysis of basolateral and apical plasma membrane fractions in mouse liver quantified the protein expression of 1373 proteins. The basolateral/apical ratios of the protein expression levels were compared with the reported immunohistochemical localization for 41 model proteins (23 basolateral, 11 apical and 7 both membrane-localized proteins). Three groups were perfectly distinguished. Border lines to distinguish the apical-, both- and basolateral locaBiomedicinesSWATH-Based Comprehensive Determination of the Localization of Apical and Basolateral Membrane Proteins Using Mouse Liver as a Model Tissue.PMC8962430N/AKAKENHI: 20H05495KAKENHI: 18KK0446KAKENHI: 20H04690KAKENHI: 20H03399Hirano SUchida YGoto RfalseSWATH-Based Comprehensive Determination of the Localization of Apical and Basolateral Membrane Proteins Using Mouse Liver as a Model Tissue.The purpose of this study was to develop a method to comprehensively determine the localization of apical and basolateral membrane proteins, using a combination of apical/basolateral membrane separation and accurate SWATH (<b>S</b>equential <b>W</b>indow <b>A</b>cquisition of all <b>TH</b>eoretical fragment ion spectra) proteomics. The SWATH analysis of basolateral and apical plasma membrane fractions in mouse liver quantified the protein expression of 1373 proteins. The basolateral/apical ratios of the protein expression levels were compared with the reported immunohistochemical localization for 41 model proteins (23 basolateral, 11 apical and 7 both membrane-localized proteins). Three groups were perfectly distinguished. Border lines to distinguish the apical-, both- and basolateral loca2022-01-01T00:00:00Z2022 Feb2026-04-08T17:56:23.731Z2025-04-05T15:22:58.426ZS-EPMC89624303520359210.3390/biomedicines10020383