PXD054601

PXD054601 is an original dataset announced via ProteomeXchange.

Title	Episodic Transport of Protein Aggregates Achieves a Positive Size Selectivity in Aggresome Formation
Description	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.
HostingRepository	PRIDE
AnnounceDate	2025-07-16
AnnouncementXML	Submission_2025-07-16_11:35:09.470.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD054601
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Kevin Dong
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-05 08:26:42	ID requested
⏵ 1	2025-07-16 11:35:09	announced

10.6019/PXD054601;

submitter keyword: LC-MS,IP

Ying Lu
contact affiliation	Harvard Medical School
contact email	Ying_Lu@hms.harvard.edu
lab head
Kevin Dong
contact affiliation	Harvard Medical School
contact email	kevindong@g.harvard.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD054601

PRIDE project URI

• PRIDE
  1. PXD054601
     1. Label: PRIDE project
     2. Name: Episodic Transport of Protein Aggregates Achieves a Positive Size Selectivity in Aggresome Formation