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PXD054430

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
DescriptionThis 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.
HostingRepositoryMassIVE
AnnounceDate2024-08-02
AnnouncementXMLSubmission_2024-08-02_06:29:00.103.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterDaniel Vogele
SpeciesList scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090;
ModificationListTMT6plex
InstrumentQ Exactive Plus
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-07-31 04:32:57ID requested
12024-08-02 06:29:00announced
Publication List
no publication
Keyword List
submitter keyword: Protein Complex Dynamics, Size Exclusion Chromatography, Degradomic Profiling, Bone Marrow-Derived Dendritic Cells
Contact List
Prof. Oliver Schilling
contact affiliationInstitute for Surgical Pathology, University Medical Center Freiburg
contact emailoliver.schilling@mol-med.uni-freiburg.de
lab head
Daniel Vogele
contact affiliationInstitute of Surgical Pathology, AG Schilling
contact emaildaniel.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/