On the standardization of ZooMS nomenclature,Journal of Proteomics

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On the standardization of ZooMS nomenclature
Journal of Proteomics ( IF 2.8 ) Pub Date : 2020-11-05 , DOI: 10.1016/j.jprot.2020.104041
Samantha Brown ₁ , Katerina Douka ₁ , Matthew J Collins ₂ , Kristine Korzow Richter ₁

Affiliation

Zooarchaeology by Mass Spectrometry (ZooMS) is rapidly becoming a staple in archaeological and cultural heritage science. Developed a decade ago, this peptide mass fingerprinting technique is expanding from a small group of researchers mainly involved in method development to a broader group of scientists using it as another tool in their toolboxes. With new researchers beginning to use the method, it is imperative that a user-friendly, standardized approach be established. A major barrier has been the often haphazard and changing nomenclature used to label peptide markers necessary for taxonomic identification. Consistent, reliable, and easy-to-understand nomenclature is key to the growth of ZooMS, particularly as the reference library continues to expand. We propose a new set of standardized guidelines for peptide markers based on their position in the type I collagen sequence from the beginning of the highly conserved, helical region. Since this region has no insertions or deletions over a wide range of taxonomic groups, the proposed nomenclature system can be used reliably and consistently across all vertebrate taxa. We propose to label ZooMS peptide markers with the gene, followed by the position of the first and last amino acid of the marker from the start of the helical region.

Significance statement

We propose a standardized nomenclature system for ZooMS peptide markers that provides consistent labels across multiple, broad taxonomic groups. This system unambiguously locates the marker peptides in the type I collagen sequence, avoids duplication of marker names, and facilitates the creation of large ZooMS databases which can include all vertebrates.

中文翻译：

关于ZooMS术语的标准化

质谱的动物考古学（ZooMS）迅速成为考古和文化遗产科学的主要内容。十年前开发的这种肽质量指纹技术已从一小群主要从事方法开发的研究人员扩展到更多的科学家，他们将其用作工具箱中的另一种工具。随着新的研究人员开始使用该方法，必须建立一种用户友好的标准化方法。一个主要的障碍是经常用来标记分类学鉴定所必需的肽标记物的偶然性和不断变化的命名法。一致，可靠且易于理解的命名法是ZooMS增长的关键，特别是随着参考库的不断扩展。我们从高度保守的螺旋区域的开始，根据它们在I型胶原蛋白序列中的位置，为肽标记物提出了一套新的标准化指南。由于该区域在广泛的分类学类别中没有插入或缺失，因此建议的命名系统可以在所有脊椎动物分类群中可靠且一致地使用。我们建议用该基因标记ZooMS肽标记，然后从螺旋区域的开始标记标记的第一个和最后一个氨基酸。