PXD032904-2

PXD032904 is an original dataset announced via ProteomeXchange.

Title	A proteomic roadmap of ribosome heterogeneity during human embryonic stem cell differentiation
Description	Recent findings suggest that the ribosome itself modulates gene expression. However, whether ribosomes change composition across cell types to control cell fate remains unknown. To determine the magnitude of ribosome heterogeneity and its functional contribution to cell fate specification, we measured ribosomal protein abundance in actively translating ribosomes by quantitative mass spectrometry on a day-by-day basis as human embryonic stem cells differentiate in a step-wise fashion down endoderm and mesoderm lineages. We identified numerous core ribosomal proteins (RPs) as changing significantly in abundance in actively translating ribosomes during cell fate specification, including progressive decreases in ribosome incorporation for several ribosomal proteins during mesoderm differentiation. We further traced ribosome composition changes at the cytoplasmic, whole-cell, and mRNA transcript levels and identified multiple mechanisms regulating actively translating ribosome composition. These findings reveal extensive ribosomal remodeling during differentiation, suggesting that individual ribosomal components may have cell type-specific specialized translation functions.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:55:55.732.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Naomi Genuth
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-02 10:45:15	ID requested
1	2022-09-19 14:30:52	announced
⏵ 2	2023-11-14 08:55:56	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: differentiation, ribosome, tandem mass tags (TMT),human embryonic stem cell

Maria Barna
contact affiliation	Stanford University
contact email	mbarna@stanford.edu
lab head
Naomi Genuth
contact affiliation	Stanford University
contact email	ngenuth@stanford.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/2022/09/PXD032904

PRIDE project URI

• PRIDE
  1. PXD032904
     1. Label: PRIDE project
     2. Name: A proteomic roadmap of ribosome heterogeneity during human embryonic stem cell differentiation