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Testing the efficacy and comparability of ZooMS protocols on archaeological bone
Journal of Proteomics ( IF 3.3 ) Pub Date : 2020-12-15 , DOI: 10.1016/j.jprot.2020.104078
Wang Naihui 1 , Brown Samantha 1 , Ditchfield Peter 2 , Hebestreit Sandra 1 , Kozilikin Maxim 3 , Luu Sindy 4 , Wedage Oshan 5 , Grimaldi Stefano 6 , Chazan Michael 7 , Horwitz Kolska Liora 8 , Spriggs Matthew 9 , Summerhayes Glenn 10 , Shunkov Michael 3 , Richter Korzow Kristine 1 , Douka Katerina 1
Affiliation  

Collagen peptide mass fingerprinting, best known as Zooarchaeology by Mass Spectrometry (or ZooMS) when applied to archaeology, has become invaluable for the taxonomic identification of archaeological collagenous materials, in particular fragmentary and modified bone remains. Prior to MALDI-based spectrometric analysis, collagen needs to be extracted from the bone's inorganic matrix, isolated and purified. Several protocols are currently employed for ZooMS analysis, however their efficacy and comparability has not been directly tested. Here, we use four different ZooMS protocols to analyze 400 bone samples from seven archaeological sites, dating to between ~500,000–2000 years ago. One of them, single-pot solid-phase-enhance sample preparation (SP3), is used for the first time as a ZooMS protocol. Our results indicate that the least-destructive ZooMS protocol which uses an ammonium bicarbonate buffer as a means of extracting collagen is most suitable for bones with good collagen preservation, whereas the acid-based methodologies can improve success rates for bones with low-to-medium collagen preservation. Since preservation of biomolecules in archaeological bones is highly variable due to age and environmental conditions, we use the percent nitrogen by weight (%N) value as an independent semi-quantitative proxy for assessing collagen content and for predicting which bones will likely result in a successful ZooMS-based identification. We find that 0.26%N as a threshold for screening material could optimize the number of spectra which produce identifications using ZooMS.

Significance statement

We present a direct comparison of three previously published ZooMS protocols for the analyses of archaeological bones, and the first use of an SP3-based approach to ZooMS analysis. Our results show that the acid-based ZooMS protocols increase the success rate for bones with low-medium collagen preservation. We identify 0.26%N as a threshold for optimizing the number of samples with enough collagen for successful peptide mass fingerprinting.



中文翻译:

测试ZooMS协议在考古骨骼上的功效和可比性

当应用于考古学时,胶原肽质量指纹图谱(通过质谱法(ZooMS)最著名的是动物考古学)对于考古学胶原材料(尤其是碎片和修饰的骨骸)的分类学鉴定已变得无价之宝。在基于MALDI的光谱分析之前,需要从骨骼的无机基质中提取胶原蛋白,进行分离和纯化。ZooMS分析目前采用了几种协议,但是其功效和可比性尚未经过直接测试。在这里,我们使用四种不同的ZooMS协议来分析可追溯到约500,000–2000年前的七个考古现场的400个骨骼样本。其中之一,单锅固相增强样品制备(SP3),首次作为ZooMS协议使用。我们的结果表明,使用碳酸氢铵缓冲液提取胶原蛋白的破坏性最小的ZooMS方案最适合保留良好胶原蛋白的骨骼,而基于酸的方法可以提高中低骨骼的成功率胶原蛋白的保存。由于考古骨骼中生物分子的保存因年龄和环境条件的不同而有很大差异,因此我们将氮的重量百分比(%N)值用作独立的半定量替代指标,以评估胶原蛋白含量并预测哪些骨骼可能会导致骨骼基于ZooMS的成功识别。我们发现0.26%N作为筛选材料的阈值可以优化使用ZooMS产生鉴定的光谱数量。

重要性声明

我们提出了三个以前发布的ZooMS协议用于考古骨骼分析的直接比较,以及首次使用基于SP3的方法进行ZooMS分析。我们的结果表明,基于酸的ZooMS协议可提高保存中低度胶原蛋白的骨骼的成功率。我们确定0.26%N为阈值,以优化具有足够胶原蛋白以成功进行肽质量指纹图谱的样品数量。

更新日期:2021-01-04
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