biostudies-literatureChen BScience and Technology Facilities CouncilWellcome TrustDiamond Light SourceBiotechnology and Biological Sciences Research Council1315https://www.ebi.ac.uk/biostudies/studies/S-EPMC12466997biostudies-literatureUnknown15(9)Detergent solubilisation remains the most commonly used but potentially problematic method to extract membrane proteins from lipid bilayers for Cryo-EM studies. Although recent advances have introduced excellent alternatives-such as amphipols, nanodiscs and SMALPs-the use of detergents is often necessary for intermediate steps. In this paper, we share our experiences working with detergent-solubilised samples within the modern Cryo-EM structural pipeline from the perspective of an EM specialist. Our aim is to inform novice users about potential challenges they may encounter. Drawing on specific examples from a variety of biological membrane systems, including Magnesium channels, lipopolysaccharide biosynthesis, and the human major facilitator superfamily transporters, we describe how the iBiomoleculesComing Clean and Avoiding Bubble Trouble-Using Detergents Wisely in the Purification of Membrane Proteins for Cryo-EM Studies.PMC12466997223727/Z/21/ZNR-27436 & NT-33941NR-27436 & NT-33941ALERT 2020 BB/T017643/1BB/T017643/1BAG 29255 & 36408BAG 29255 & 36408Ford RCHarrison PKargas VCollins RFPollock NPrince SMChen BfalseComing Clean and Avoiding Bubble Trouble-Using Detergents Wisely in the Purification of Membrane Proteins for Cryo-EM Studies.Detergent solubilisation remains the most commonly used but potentially problematic method to extract membrane proteins from lipid bilayers for Cryo-EM studies. Although recent advances have introduced excellent alternatives-such as amphipols, nanodiscs and SMALPs-the use of detergents is often necessary for intermediate steps. In this paper, we share our experiences working with detergent-solubilised samples within the modern Cryo-EM structural pipeline from the perspective of an EM specialist. Our aim is to inform novice users about potential challenges they may encounter. Drawing on specific examples from a variety of biological membrane systems, including Magnesium channels, lipopolysaccharide biosynthesis, and the human major facilitator superfamily transporters, we describe how the i2025-01-01T00:00:00Z2025 Sep2026-06-30T03:22:51.077Z2026-06-30T03:15:54.121ZS-EPMC124669974100862210.3390/biom15091315