PXD031832-1
PXD031832 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling Studies |
| Description | In spite of its central role in biology and disease, protein turnover is a largely understudied aspect of most proteomic studies due to the complexity of computational workflows that analyze in-vivo turnover rates. To address this need, we developed a new computational tool, TurnoveR, to accurately calculate protein turnover rates from mass spectrometric analysis of metabolic labeling experiments in Skyline, a free and open-source proteomics software platform. TurnoveR is a straightforward graphical interface that enables seamless integration of protein turnover analysis into a traditional proteomics workflow in Skyline, allowing users to take advantage of the advanced and flexible data visualization and curation features built into the software. The TurnoveR computational pipeline performs critical steps to determine protein turnover rates, including isotopologue demultiplexing, precursor-pool correction, statistical analysis, and generation of data reports and visualizations. This workflow is compatible with many mass spectrometric platforms and re-capitulates turnover rates and differential changes in turnover rates between treatment groups calculated in previous studies. We expect that the addition of TurnoveR to the widely used Skyline proteomics software will facilitate wider utilization of protein turnover analysis in highly relevant biological models, including aging, neurodegeneration, and skeletal muscle atrophy. |
| HostingRepository | MassIVE |
| AnnounceDate | 2022-02-22 |
| AnnouncementXML | Submission_2022-02-22_11:04:39.022.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Nate |
| SpeciesList | scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090; |
| ModificationList | Oxidation; 3x(2)H labeled L-leucine |
| Instrument | LTQ Orbitrap Velos; TripleTOF 6600 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2022-02-22 09:56:18 | ID requested | |
| ⏵ 1 | 2022-02-22 11:04:39 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: protein turnover, proteostasis, aging, data-dependent acquisition, metabolic labeling, stable isotope labeling |
Contact List
| Birgit Schilling | |
|---|---|
| contact affiliation | Buck Institute |
| contact email | bschilling@buckinstitute.org |
| lab head | |
| Nate | |
| contact affiliation | The Buck Institute for Research on Aging |
| contact email | nbasisty@buckinstitute.org |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive.ucsd.edu/MSV000088893/ |
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