Department of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States.
Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
Chem Rev. 2022 Aug 24;122(16):13401-13446. doi: 10.1021/acs.chemrev.1c00703. Epub 2022 Jul 15.
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
古蛋白质组学是分子生物学、古生物学、考古学、古生态学和历史学交叉领域的一个快速发展的领域。古蛋白质组学研究利用蛋白质的长寿性和多样性来探索过去的基本问题。虽然它的起源可以追溯到 DNA 的特征描述之前，但只有随着软电离质谱技术的出现，古代蛋白质的研究才真正成为可能。在过去的 20 年中，技术的进步为更好地理解在考古学和古生物学记录中发现的丰富古代蛋白质生物档案的保存、降解和恢复提供了越来越多的机会。古蛋白质组学从 90 年代少数关于单个高度丰富的古代蛋白质的研究发展而来，如今已成为一个不断发展的领域，其应用范围广泛，从高度碎片化的骨骼和贝壳的分类鉴定、灭绝物种的系统发育解析，到从牙垢和陶器食物残渣中探索过去的烹饪方法以及过去疾病的特征，都有涉及。更广泛地说，这些研究为理解过去的人类-动物相互作用、过去环境和环境变化的重建、通过大规模筛选非诊断性骨碎片扩大人类化石记录、以及脊椎动物化石记录的系统发育解析打开了新的大门。尽管取得了这些进展，但大部分古代蛋白质组学记录仍未被探索。在这里，我们概述了该领域的历史，总结了目前使用的主要方法和应用，并对当前的挑战进行了批判性评估。最后，我们展望未来，创新的解决方案和新兴技术将在使我们能够访问尚未探索的“黑暗”蛋白质组学方面发挥重要作用，从而更全面地理解古代蛋白质在解释过去方面所起的作用。
