Comparing the Use of Magnetic Beads with Ultrafiltration for Ancient Dental Calculus Proteomics.

SP3 acetone precipitation ancient dairy protein casein dental calculus proteome ultrafiltration β-lactoglobulin

Journal

Journal of proteome research
ISSN: 1535-3907
Titre abrégé: J Proteome Res
Pays: United States
ID NLM: 101128775

Informations de publication

Date de publication:
05 03 2021
Historique:
pubmed: 18 2 2021
medline: 22 6 2021
entrez: 17 2 2021
Statut: ppublish

Résumé

Over the past two decades, proteomic analysis has greatly developed in application to the field of biomolecular archaeology, coinciding with advancements in LC-MS/MS instrumentation sensitivity and improvements in sample preparation methods. Recently, human dental calculus has received much attention for its well-preserved proteomes locked in mineralized dental plaque which stores information on human diets and the oral microbiome otherwise invisible to other biomolecular approaches. Maximizing proteome recovery in ancient dental calculus, available only in minute quantities and irreplaceable after destructive analysis, is of paramount importance. Here, we compare the more traditional ultrafiltration-based and acetone precipitation approaches with the newer paramagnetic bead approach in order to test the influence of demineralization acid on recovered proteome complexity obtained from specimens as well as the sequence coverages matched for significant proteins. We found that a protocol utilizing EDTA combined with paramagnetic beads increased proteome complexity, in some cases doubling the number of unique peptides and number of proteins matched, compared to protocols involving the use of HCl and either acetone precipitation or ultrafiltration. Although the increase in the number of proteins was almost exclusively of bacterial origin, a development that has implications for the study of diseases within these ancient populations, an increase in the peptide number for the dairy proteins β-lactoglobulin and casein was also observed reflecting an increase in sequence coverage for these dietary proteins of interest. We also consider structural explanations for the discrepancies observed between these two key dietary proteins preserved in archaeological dental calculus.

Identifiants

pubmed: 33596076
doi: 10.1021/acs.jproteome.0c00862
doi:

Substances chimiques

Proteome 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1689-1704

Auteurs

Karren S Palmer (KS)

School of Natural Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.

Cheryl A Makarewicz (CA)

Institute for Prehistoric and Protohistoric Archaeology, Kiel University, Johanna-Mestorf Strasse 2-6, D-24118 Kiel, Germany.

Alexey A Tishkin (AA)

Department of Archeology, Ethnography, and Museology, Altai State University, Lenin Prospect 61, 656049 Barnaul, Russia.

Svetlana S Tur (SS)

Department of Archeology, Ethnography, and Museology, Altai State University, Lenin Prospect 61, 656049 Barnaul, Russia.

Amartuvshin Chunag (A)

Mongolian Institute of Archaeology, Ulaanbaatar 13343, Mongolia.

Erdenebaatar Diimajav (E)

Department of Archaeology and History, Ulaanbataar State University, Luvsantseveen Street, 5th khoroo, 15th khorgoolol, Bayanzurk District 13343 Ulaanbaatar, Mongolia.

Bayarsaikhan Jamsranjav (B)

National Museum of Mongolia, Ulaanbaatar Mongolia, Juulchin Street-1, Ulaanbaatar 13343, Mongolia.

Michael Buckley (M)

School of Natural Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.

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Classifications MeSH