This dataset comprises raw quantitative proteomics data processed abundance values heatmaps volcano plot statistics figure datasets and day-wise normalized protein expression profiles from a comparative proteomics study of murine skin wound healing following biomaterial treatment. The study used bottom-up LC-MS/MS proteomics to track temporal protein and pathway changes across three conditions (collagen hydrogel LMAP DMAP) at inflammation proliferation and resolution stages in SKH-1 mouse wounds. Key data were generated using Orbitrap Exploris 240 instrumentation SEQUEST HT/Proteome Discoverer 2.5 for peptide identification and quantification and multiple bioinformatics pipelines (STRING clusterProfiler MatrisomeAnalyzer Heatmapper.ca). In vivo experimental design histological and imaging protocols details of normalization imputation outlier detection and statistical analysis approaches are documented in the manuscript. Supporting files in this repository include CSV spreadsheets for protein abundances and volcano plots per day Excel summaries for heatmaps and figure data plus raw and processed data tables. Associated MS/MS raw files are stored in PRIDE: PXD067152
