Isolation, enrichment and identification of p62 condensates components by GFP-Trap Agarose Beads pulldown followed by Label Free and Tandem Mass Tag (TMT) mass spectrometry analysis from Hap1 cells

Selective autophagy contributes to the removal of harmful proteins from the cytoplasm. This cargo material is selected by cargo receptors such as p62/SQSTM1 and finally degraded. However, the molecular composition of the p62 condensates and therefore the nature of the cargo delivered by them is incompletely understood. In order to obtain insights into their composition, we have developed a method to isolate these condensates followed by TMT and Label Free mass spectrometry-based identification of their protein content.