PXD051940
PXD051940 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | TermineR: extracting information on proteolytic processing from shotgun proteomics data |
| Description | TermineR is a data analysis approach for the analysis of proteolytic processing from shotgun proteomics data, wrapped up in an R package currently available on Github. This repo contains raw data used to showcase this approach. We used a model of polycystic kidney disease (PKD) in mice to showcase this approach (KO -> PKD, vs WT). After protein extraction and reductive alkylation, samples were treated with TMT16plex for labelling of protein N-termini and cleavage events; then digested with trypsin. Measurements of this experiment were performed via Q-Exactive plus and searched using FragPipe. To evaluate the potential effect of protein extraction methods on the identification of cleavage events, we performed a pilot experiment with samples from the same PKD model. Tissues from 3 mice for each condition (KO or WT) were subjected to protein extraction using beat beating, and two sonication approaches. Then processed with trypsin and measured in label-free DIA model in a timsTOF flex and searched in Spectronaut. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-07-22 |
| AnnouncementXML | Submission_2024-07-22_04:23:46.495.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Miguel Cosenza-Contreras |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090; |
| ModificationList | TMTpro; Acetyl; Carbamidomethyl |
| Instrument | Q Exactive Plus; timsTOF fleX |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-05-02 04:37:56 | ID requested | |
| ⏵ 1 | 2024-07-22 04:23:46 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: proteolysis, terminomics, data processing, polycystic kidney disease |
Contact List
| Prof. Oliver Schilling | |
|---|---|
| contact affiliation | Institute for Surgical Pathology, University Medical Center Freiburg |
| contact email | oliver.schilling@mol-med.uni-freiburg.de |
| lab head | |
| Miguel Cosenza-Contreras | |
| contact affiliation | UNIVERSIT�TSKLINIKUM FREIBURG |
| contact email | miguel.de.jesus.cosenza.contreras@uniklinik-freiburg.de |
| 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/v07/MSV000094661/ |
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