Response to Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry"

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Abstract
We sequenced six endogenous collagen peptides from Tyrannosaurus rex bone fragments using mass spectrometry. Five sequences match birds, but only two match amphibians, supporting dinosaur-bird relationships. Buckley et al. reinterpret and misinterpret our data and question sequence authenticity, but they used a suboptimal phylogenetic algorithm to analyze only a subset of reported sequences and they suggest analyses that are less sensitive and less specific than mass spectrometry. We disagree and use data to explain.