Mass spectrometry, Bayesian phylogenetic, and stable isotope data for ZooMS analysis of Unangax̂ whale bone (Attu and Chernabura Islands, Aleutian Islands, Alaska)

This repository contains the primary data supporting Miller et al., ZooMS and Stable Isotope Analysis of Unangax̂ Whale Bone Structures Uncover Human–Cetacean Ecology in the Aleutian Islands, Alaska. The study reports the biomolecular analysis of Unangax̂ (Aleut) zooarchaeological cetacean material, combining collagen peptide mass fingerprinting (ZooMS), shotgun proteomics, stable carbon and nitrogen isotope analysis, clade-specific mitochondrial D-loop amplification, and AMS radiocarbon dating of 14 worked and fragmentary cetacean bone specimens from Attu (ATU-014; n=10) and Chernabura (XSI-00007; n=4) Islands, spanning 240 BC to AD 1120. The deposit contains: 1) Thermo .raw LC-MS/MS files (ms_ms_raw_files.zip) from trypsin-digested bone collagen (ECBM_QE019866–ECBM_QE019892); 2) Supplementary_Materials_2.zip contains both Sequest HT reference FASTA files that include a whole-collagen UniProtKB export (391,316 sequences, 14,328 species) and a taxonomically restricted cetacean-only database (11,698 sequences, 54 species), the cRAP contaminant panel, and Sequest HT per-specimen search outputs for both Sequest HT matches; 3) complete BEAST X v10.5.0 files (alignments, XML, posterior logs and tree samples, MCC trees) for the masked and unmasked placement of a 273 bp Eubalaena japonica control-region amplicon from Attu specimen 181780, under HKY+I with an uncorrelated lognormal relaxed clock and a constant-size coalescent prior; and 4) BLASTn top 100 hits for the mtDNA control-region amplicon, and .csv containing all cetacean comparative isotope data.