PXD054545-1

PXD054545 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, Dynabeads Protein G beads (Thermo Fisher, #10004D) were used to immunoprecipitate different forms of purified AgDD proteins through an HA-tag on the AgDD after incubating AgDD proteins in the Xenopus egg extract. AgDD samples used in the study include AgDD aggregates formed in the extract (AgDDXE), in the physiological buffer (AgDDpb) and the unaggregated control (AgDDsol). Two batches of actin-depolymerized CSF extracts were freshly prepared in parallel and used for experiments as repeats. 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 Fusion Lumos instrument (using hrMS2-mode). 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_11:37:27.957.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD054545
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Kevin Dong
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-02 11:48:59	ID requested
⏵ 1	2025-07-16 11:37:28	announced

10.6019/PXD054545;

submitter keyword: Xenopus, IP

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

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PRIDE project URI

• PRIDE
  1. PXD054545
     1. Label: PRIDE project
     2. Name: Episodic Transport of Protein Aggregates Achieves a Positive Size Selectivity in Aggresome Formation