MassIVE MSV000097308

Partial Public PXD061792

Proteome analysis of Corynebacterium diphtheriae - macrophage interaction

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Description

Contact of Corynebacterium diphtheriae with macrophages induce adaptations on both bacterial and cellular sides. Using an experimental design involving gentamicin protection and liquid chromagraphy followed by mass-spectrometry, a multi-species proteomic dataset was analyzed at different time points of the infection assay. Several previously undescribed Corynebacterium proteins were differentially regulated, as well as key macrophage components of the phagolysosome. Overall, Bacteria responded to phagocytosis by changes in DNA repair, transcription and cell wall synthesis proteins, while macrophages showed changes in components of the innate immune system. This dataset consists of: - ThermoFisher's .raw files of three biological replicates of the infection assays (total proteome mixture of bacteria and eukaryotic cells and tagged using TMT-10). They can be downloaded all at once via the .zip file. - Protein abundance data for Macrophage THP-1 cells (M0) obtained by LC-MS/MS followed by peptide sequencing using Proteome Discoverer (ThermoFisher) -see .zip folder. - Protein abundance data for Macrophage C. diphtheriae ISS3319 (CD) obtained by LC-MS/MS followed by peptide sequencing using Proteome Discoverer (ThermoFisher) - see .zip folder. - Differential protein abundance analysis for CD and M0 using LIMMA. - Data underlying the growth curves observed in CD in RPMI + 10% FBS conditions (infection assay conditions). - BLASTP searches, PFAM clans, and InterPro annotations for CD. - STRING-based PPI network (baseline) and APSPs between differentially abundant proteins in CD. - Related R scripts. [doi:10.25345/C5N01059C] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Host-pathogen interaction ; Microbiology ; Macrophage, THP-1 Null cells ; Gentamicin protection assay ; Corynebacterium diphtheriae ; Diphtheria ; DatasetType:Proteomics

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Principal Investigators:
(in alphabetical order) 		Andreas Burkovski, Friedrich-Alexander-Universitaet Erlangen-Nuernberg (FAU), Germany
Submitting User: Muszeb
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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.