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  Testing the efficacy and comparability of ZooMS protocols on archaeological bone

Wang, N., Brown, S., Ditchfield, P., Hebestreit, S., Kozilikin, M., Sindy, L., et al. (2021). Testing the efficacy and comparability of ZooMS protocols on archaeological bone. Journal of Proteomics, 233: 104078. doi:10.1016/j.jprot.2020.104078.

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Wang, Naihui1, Author              
Brown, Samantha1, 2, Author              
Ditchfield, Peter, Author
Hebestreit, Sandra1, Author              
Kozilikin, Maxim, Author
Sindy, Luu, Author
Wedage, Oshan1, Author              
Stefano, Grimaldi, Author
Chazan, Michael, Author
Horwitz Kolska, Liora, Author
Spriggs, Matthew, Author
Summerhayes, Glenn, Author
Shunkov, Michael, Author
Richter, Kristine Korzow1, Author              
Douka, Katerina1, Author              
1Archaeology, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074312              
2FINDER, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2541700              


Free keywords: Palaeoproteomics, ZooMS, Collagen, Bone, Nitrogen
 Abstract: 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.


Language(s): eng - English
 Dates: 2020-12-122021-02-20
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: 1. Introduction
1.1. ZooMS protocols
1.2. Screening methods for bone collagen preservation

2. Materials and methods
2.1. Materials
2.2. Reagents and software
2.3. Measuring %N
2.4. Experimental design for ZooMS protocols
2.5. Methods: collagen extraction protocols
2.5.1. Phase 1
2.5.2. Phase 2
2.5.3. Phase 3
2.7. Peptide mass spectra data analysis

3. Results
3.1. Nitrogen percentage
3.2. ZooMS results

4. Discussion
4.1. Correlation of %N with number of peptide peaks
4.2. Assessment of the extraction protocols

5. Conclusions
 Rev. Type: Peer
 Identifiers: DOI: 10.1016/j.jprot.2020.104078
Other: shh2816
 Degree: -



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Title: Journal of Proteomics
  Abbreviation : J. Proteome
Source Genre: Journal
Publ. Info: Amsterdam, The Netherlands : European Proteomics Association & Elsevier
Pages: - Volume / Issue: 233 Sequence Number: 104078 Start / End Page: - Identifier: ISSN: 1874-3919
CoNE: https://pure.mpg.de/cone/journals/resource/1874-3919