PXD054300

PXD054300 is an original dataset announced via ProteomeXchange.

Title	RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues, cancer cells, and macrophages - label-free MS RAPIDASH of L36-FLAG and S17-FLAG E14 mESCs
Description	Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translation. Nevertheless, a lack of technologies to enrich RAPs across sample types has prevented systematic analysis of RAP identities, dynamics, and functions. We have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including DHX30 and LLPH, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development linked to the translation of genes with long coding sequences. In addition, we showed RAPIDASH can identify ribosome changes in cancer cells. Finally, we characterized ribosome composition remodeling during immune cell activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs in multiple cell types, tissues, and stimuli and is adaptable to characterize ribosome remodeling in several contexts. This dataset refers to label-free identification of RAPs enriched by RAPIDASH from L36-FLAG and S17-FLAG mouse embryonic stem cells (mESCs). This dataset is used for comparison with Ribo-FLAG IP and elaborated in Figures 1G-H.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:58:07.454.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD054300
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Teodorus Theo Susanto
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-27 23:28:16	ID requested
1	2024-09-11 18:51:46	announced
⏵ 2	2024-10-22 06:58:07	announced	2024-10-22: Updated project metadata.

10.6019/PXD054300;

10.1016/J.MOLCEL.2024.08.023;

submitter keyword: acquity UPLC M-class system, embryonic stem cell, orbitrap elite, Ribo-FLAG immunoprecipitation,ribosome, ribosome-associated proteins, mouse

Maria Barna
contact affiliation	Associate Professor of Genetics Stanford University USA
contact email	mbarna@stanford.edu
lab head
Teodorus Theo Susanto
contact affiliation	Scientist
contact email	theosusanto@protonmail.com
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/2024/09/PXD054300

PRIDE project URI

• PRIDE
  1. PXD054300
     1. Label: PRIDE project
     2. Name: RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues, cancer cells, and macrophages - label-free MS RAPIDASH of L36-FLAG and S17-FLAG E14 mESCs