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Size Exclusion Chromatography Based Proteomic and Degradomic Profiling of Inflammasome-Activated, Murine Bone Marrow-Derived Dendritic Cells

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Prof. Oliver Schilling

PROVIDER: MSV000095490 | MassIVE | Wed Jul 31 04:32:00 BST 2024

SECONDARY ACCESSION(S): PXD054430

REPOSITORIES: MassIVE

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