PXD054298 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues, cancer cells, and macrophages - TMT MS RAPIDASH comparison with sucrose cushion of 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 relative quantification of ribosome associated protein enriched from sucrose cushion and RAPIDASH, as elaborated in Figure 1D, S3B, and S3C. |
| HostingRepository | PRIDE |
| AnnounceDate | 2024-10-22 |
| AnnouncementXML | Submission_2024-10-22_06:58:07.498.xml |
| DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD054298 |
| 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 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2024-07-27 19:58:30 | ID requested | |
| 1 | 2024-09-11 18:50:25 | announced | |
| ⏵ 2 | 2024-10-22 06:58:07 | announced | 2024-10-22: Updated project metadata. |
Publication List
Keyword List
| submitter keyword: acquity UPLC M-class system, orbitrap elite, sucrose cushion,ribosome, TMT MS, ribosome-associated proteins, mouse |
Contact List
| 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 | |
Full Dataset Link List
Dataset FTP location
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| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD054298
- Label: PRIDE project
- Name: RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues, cancer cells, and macrophages - TMT MS RAPIDASH comparison with sucrose cushion of E14 mESCs
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