This repository contains the input and processed datasets used in the study “Comparative mitochondrial proteomics across the tree of life reveals evolutionary, functional, and therapeutic insights”, part of the MitoCarta Tree of Life (MitoTOL) project. The dataset spans 673 eukaryotic species and 34 downsampled prokaryotic groups and supports analyses of mitochondrial protein evolution, orthogroup inference, phylogenetic profiling, ancestral reconstructions, and eukaryogenesis timing. The archive includes: data.tar.gz — Primary datasets organized by analysis type, including orthogroup inference, phylogenetically-resolved orthogroup inference, DeepLoc retraining and prediction, phylogenetic profiling, taxonomic metadata, HGT, and reconstruction outputs. alignments_and_initial_trees.tar.gz — Protein FASTA files, multiple sequence alignments, and maximum-likelihood phylogenies for each orthogroup. pruned_rooted_trees.tar.gz — Pruned and rooted trees used for downstream reconciliation and timing analyses. reconciled_consensus_trees_with_supports.tar.gz — Reconciled consensus protein trees with optimized branch lengths and node support values, along with pruned MSAs used to infer branch lengths. reconciled_consensus_trees_for_Archaeplastida_timing.tar.gz — Reconciled consensus protein trees with optimized branch lengths for Archaeplastida-level timing inferences. reconciled_consensus_trees_for_LECA_timing.tar.gz — Reconciled consensus protein trees with optimized branch lengths for LECA-level timing analyses. reconciled_consensus_trees_branch_length_optimization_with_supports.tar.gz — AleRax reconciliation outputs, including samples of reconciled trees and majority-rule consensus trees. species_fastas.tar.gz — Protein FASTA files for all eukaryotic species and prokaryotic groups included in the study. All datasets follow consistent naming conventions (e.g., [Orthogroup_ID], [PhROG_ID], [TAXONOMY_ID]). Detailed documentation of file contents is provided in the accompanying README.txt. The full computational workflow, including scripts for alignment, tree inference, reconciliation, phylogenetic profiling, and ancestral reconstructions, is available at:https://github.com/michaelzhuchen/mito-evolution Please cite this dataset using 10.5281/zenodo.17823714.