PXD054430-1

PXD054430 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Size Exclusion Chromatography Based Proteomic and Degradomic Profiling of Inflammasome-Activated, Murine Bone Marrow-Derived Dendritic Cells
Description	This proteomic dataset explores the formation of protein complexes during inflammasome activation in bone marrow-derived dendritic cells (BMDCs) from gasdermin D-deficient mice. The study employs size exclusion chromatography (SEC) linked with mass spectrometry-based proteomics to provide a global overview of protein complexes and their dynamics, with a particular focus on proteolytic enzymes and truncated proteins in higher molecular weight complexes. BMDCs were cultured and differentiated using GM-CSF, then primed with LPS and treated with either nigericin or Val-boroPro (Talabostat). Proteins were separated by SEC, and fractions were labelled with tandem mass tags (TMT). The labelled fractions were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Raw mass spectrometry data were processed using the FragPipe pipeline (v20.0) with semi-specific tryptic cleavage specificity allowing one missed cleavage. Fixed modifications included carbamidomethylation at cysteines and a TMT mass delta of 229.16293 at lysines, while N-terminal acetylation and N-terminal TMT mass delta were set as variable modifications. Normalization across SEC fractions was performed using the reference channel in R (v4.1.0) within Rstudio, followed by further analysis of the processed data.
HostingRepository	MassIVE
AnnounceDate	2024-08-02
AnnouncementXML	Submission_2024-08-02_06:29:00.103.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Daniel Vogele
SpeciesList	scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090;
ModificationList	TMT6plex
Instrument	Q Exactive Plus

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-31 04:32:57	ID requested
⏵ 1	2024-08-02 06:29:00	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: Protein Complex Dynamics, Size Exclusion Chromatography, Degradomic Profiling, Bone Marrow-Derived Dendritic Cells

submitter keyword: Protein Complex Dynamics, Size Exclusion Chromatography, Degradomic Profiling, Bone Marrow-Derived Dendritic Cells

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
Daniel Vogele
contact affiliation	Institute of Surgical Pathology, AG Schilling
contact email	daniel.vogele@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/v08/MSV000095490/

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/v08/MSV000095490/