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.

中文翻译：

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古蛋白质组学

古蛋白质组学是对古代蛋白质的研究，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寿命和多样性来探索有关过去的基本问题。虽然它的起源早于 DNA 的表征，但直到软电离质谱的出现，对古代蛋白质的研究才真正变得可行。过去 20 年的技术进步让我们有更多机会更好地了解考古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。古蛋白质组学源于 20 世纪 90 年代对单个高度丰富的古代蛋白质的少量研究，如今是一个不断扩展的领域，具有多种应用，从高度碎片化的骨骼和贝壳的分类学鉴定、灭绝物种的系统发育解析到对过去的美食的探索。牙结石和陶器食物结皮以及过去疾病的特征。更广泛地说，这些研究为理解过去的人类与动物的相互作用、过去环境和环境变化的重建、通过大规模筛选非诊断性骨骼碎片来扩展古人类化石记录以及脊椎动物化石的系统发育解析打开了新的大门。记录。即使有了这些进步，许多古代蛋白质组学记录仍然未被探索。在这里，我们概述了该领域的历史，总结了当前使用的主要方法和应用，并对当前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发挥重要作用，使我们能够获得尚未探索的“黑暗”蛋白质组，从而更全面地了解古代蛋白质在解释蛋白质组中可以发挥的作用。过去的。