The ancient preserved molecules offer the opportunity to gain a better knowledge on the biological past. In recent years, bones proteomics has become an attractive method to study the animal biological origin, extinct species and species evolution as an alternative to DNA analysis which is limited by DNA amplification present in ancient samples and its contamination. However, the development of a proteomic workflow remains a challenge. The analysis of fossils must consume a low quantity of material to avoid damaging the samples. Another difficulty is the absence of genomic data for most of the extinct species. In this study, a proteomic methodology was applied to mammalian bones of 130,000 years old from the earlier Upper Pleistocene site of Scladina Cave (Belgium). Starting from 5 milligram samples, our results show a large majority of detected peptides matching collagen I alpha 1 and alpha 2 proteins with a sequence coverage up to 60%. Using sequence homology with modern sequences, a biological classification was successfully achieved and the associated taxonomic ranks to each bone were identified consistently with the information gained from osteomorphological studies and palaeoenvironmental and palaeodietary data. Among the taxa identified are the Felidae family, Bovinae subfamily, Elephantidae family and the Ursus genus. Amino acid substitutions on the collagens were identified providing new information on extinct species sequences and also helping in taxonomy-based clustering. Considering samples with no osteomorphological information, such as two bone retouchers, proteomics successfully identified the bovidae and ursidae families providing new information to the paleontologists on these objects. Combining osteomorphology studies and amino acid variations identified by proteomics, one retoucher was identified to be potentially from the Ursus spelaeus species.

中文翻译：

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通过蛋白质组学分析无法从其骨形态学研究中识别出来自上更新世骨碎片的灭绝物种

保存下来的古老分子提供了更好地了解生物过去的机会。近年来，骨骼蛋白质组学已成为研究动物生物起源、灭绝物种和物种进化的一种有吸引力的方法，作为 DNA 分析的替代方法，DNA 分析受到古代样本中存在的 DNA 扩增及其污染的限制。然而，蛋白质组学工作流程的开发仍然是一个挑战。化石分析必须消耗少量材料以避免损坏样品。另一个困难是缺乏大多数灭绝物种的基因组数据。在这项研究中，蛋白质组学方法被应用于来自 Scladina 洞穴（比利时）较早的上更新世遗址的 130,000 年前的哺乳动物骨骼。从 5 毫克样品开始，我们的结果显示，大部分检测到的肽与 I 型胶原蛋白 alpha 1 和 alpha 2 蛋白相匹配，序列覆盖率高达 60%。使用与现代序列的序列同源性，成功地实现了生物学分类，并且与从骨形态学研究和古环境和古饮食数据中获得的信息一致地确定了每个骨骼的相关分类等级。已确定的分类群包括猫科、牛科、象科和熊属。确定了胶原蛋白上的氨基酸取代，提供了关于已灭绝物种序列的新信息，也有助于基于分类的聚类。考虑没有骨形态学信息的样本，例如两个骨修整器，蛋白质组学成功地鉴定了牛科和熊科，为古生物学家提供了有关这些物体的新信息。结合骨形态学研究和蛋白质组学鉴定的氨基酸变异，鉴定出一名修图师可能来自Ursus spelaeus物种。