Episodic Transport of Protein Aggregates Achieves a Positive Size Selectivity in Aggresome Formation

To generate this dataset, different proteins (human HDAC6, CCT8, 26S proteasome, Hsc70, Hsp90, p62, and Xenopus HOOK2 were immunoprecipitated from the Hela S3 cell extract or Xenopus egg extract by the Dynabeads Protein G beads (Thermo Fisher, #10004D) coated with corresponding primary antibodies as indicated in the original study. Proteins immunoprecipitated by the beads were determined by Tandem-Mass-Tag mass spectrometry (TMT-MS). On-bead digestion, TMTpro 16plex labeling, alkylation/cysteine protection by iodoacetamide (IAA), stage tip desalting, and SpeedVac drying were performed following the manufacturer’s instructions and standard protocols (ThermoFisher, #A44520; Zhou, et al., 2024). Peptides were reconstituted in 0.1% formic acid for LC-MS analysis. TMT-labeling efficiency was verified to be more than 95%. Mass spectrometric data were collected on an Orbitrap Exploris480 instrument. Details of data acquisition and analysis were included in the Methods part of the original work.