Autophagosome content profiling using proximity biotinylation proteomics coupled to protease digestion in mammalian cells

Published: 7 April 2021| Version 1 | DOI: 10.17632/33dx4p8d4n.1
Christian Behrends


The ascorbate peroxidase APEX2 is commonly used to study the neighborhood of a protein of interest by proximity-dependent biotinylation. Here, we describe a protocol for sample processing compatible with immunoblotting and mass spectrometry that is suitable to specifically map the content of autophagosomes and potentially other short-lived endomembrane transport vesicles without the need of subcellular fractionation. By combining live-cell biotinylation with proteinase K digestion of cell homogenates, proteins enriched in membrane-protected compartments can be readily enriched and identified. For complete details on the use and execution of this protocol, please refer to (Zellner et al., 2021).



Ludwig-Maximilians-Universitat Munchen


Confocal Microscopy, Western Blot