This dataset and associated resources support the manuscript describing Manchester Proteome Profiler (MPP), an open-source R Shiny application for downstream analysis of quantitative proteomics data. MPP enables streamlined workflows for filtering, normalization, imputation, differential expression analysis, and clustering across single or dual datasets. It integrates SAINTexpress for AP-MS and proximity labeling experiments and provides functional interpretation through Gene Ontology enrichment and protein–protein interaction networks using BioGRID and STRING. The files include: Example input datasets processed with MaxQuant and FragPipe Experimental and comparison template Key Features: Compatible with MaxQuant, FragPipe, Proteome Discoverer, and custom formats Supports complex experimental designs and two-dataset comparisons Interactive visualizations and publication-ready reports Open-source code available on GitHub: https://github.com/StuCain/Manchester_Proteome_Profiler Public server: https://mpp.sbs.manchester.ac.uk