DEP

DEP performs differential protein expression and enrichment analysis of mass spectrometry proteomics data to identify proteins with altered abundance or interaction status for comparative and ubiquitin-focused studies.

Key Features:

• Differential expression/enrichment analysis: Identifies differentially enriched proteins from quantitative proteomics datasets derived from LC-MS/MS.
• Input compatibility: Integrates with tabular outputs from quantitative analysis software such as MaxQuant and IsobarQuant and accepts tabular text file formats.
• UbIA-MS support: Supports analysis of ubiquitin interactor affinity enrichment-mass spectrometry (UbIA-MS) datasets, including experiments using biotinylated nonhydrolyzable diubiquitin baits that mimic native diubiquitin and resist deubiquitinase cleavage.
• Ubiquitin linkage coverage: Enables identification of ubiquitin interactors across all ubiquitin linkage types from crude cell lysates.
• Computational implementation: Provided as an R software package for performing the required data analyses.

Scientific Applications:

• Differential proteomics: Comparative analysis of protein abundance changes between conditions or treatments using LC-MS/MS-derived quantitative data.
• Ubiquitin interaction mapping: Identification of ubiquitin interactors and linkage-specific interactomes using UbIA-MS with nonhydrolyzable diubiquitin baits.
• Native-complex and PTM-preserving studies: Analysis of interactors captured from crude cell lysates to preserve endogenous protein levels, post-translational modifications, and native protein complex assemblies.
• Cell-type and stimulus-dependent interaction studies: Investigation of how ubiquitin interactions vary across cell types or in response to stimuli.

Methodology:

Data analysis to identify differentially enriched proteins from LC-MS/MS outputs using an R software package and tabular inputs (text files) generated by tools such as MaxQuant or IsobarQuant.