PXD051940-1

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

no publication

Keyword List

submitter keyword: proteolysis, terminomics, data processing, polycystic kidney disease

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/

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/