Dataset Information

A Comparison of Proteomic, Genomic, and Osteological Methods of Archaeological Sex Estimation

ABSTRACT: Proteomic sex estimation of human remains via liquid chromatography tandem mass spectrometry (LC- MS/MS) of sexually dimorphic amelogenin peptides in tooth enamel. The human remains analyzed in this study were recovered from two archaeological sites, Síi Túupentak (CA-ALA-565; ca. 200-600 cal BP) and Rummey Ta Kuččuwiš Tiprectak (CA-ALA-704/H; ca. 180-2240 cal. BP), Late Holocene ancestral Ohlone villages in Central California. The X and Y chromosomes code for distinctive isoforms of amelogenin proteins, AMELX_HUMAN and AMELY_HUMAN. Fragments of these proteins can be detected using shotgun liquid chromatography mass spectrometry and assigned to the AMELX or AMELY isoform. We use nano-liquid chromatography coupled with orbitrap tandem mass spectrometry (LC-orbitrap-MS/MS). Signals of all peptides that can be unambiguously attributed to either AMELY or AMELX isoforms are summed and normalized for sample weight. Confident detection of AMELY specific peptides provides an unambiguous indicator of a male sex chromosome.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Tooth Enamel

SUBMITTER: Glendon Parker

LAB HEAD: Glendon J Parker

PROVIDER: PXD016076 | Pride | 2020-07-20

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 201

Publications

A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation.

Buonasera Tammy T Eerkens Jelmer J de Flamingh Alida A Engbring Laurel L Yip Julia J Li Hongjie H Haas Randall R DiGiuseppe Diane D Grant Dave D Salemi Michelle M Nijmeh Charlene C Arellano Monica M Leventhal Alan A Phinney Brett B Byrd Brian F BF Malhi Ripan S RS Parker Glendon G

Scientific reports 20200717 1

Sex estimation of skeletons is fundamental to many archaeological studies. Currently, three approaches are available to estimate sex-osteology, genomics, or proteomics, but little is known about the relative reliability of these methods in applied settings. We present matching osteological, shotgun-genomic, and proteomic data to estimate the sex of 55 individuals, each with an independent radiocarbon date between 2,440 and 100 cal BP, from two ancestral Ohlone sites in Central California. Sex es ...[more]

PMID: 32681049

Similar Datasets

Project description:The enamel proteome includes a range of proteins which are well-preserved in archaeological settings but have so far received less study than the sex-specific sequencing of enamel. We look beyond sex-specific sequencing of amelogenin to investigate the potential of several serum proteins, including immunoglobulin gamma (IgG), the major immunoglobulin found in blood serum, and C-reactive protein (CRP) which is associated with inflammatory response, to provide insight into the health and stresses experienced by individuals in the past. We apply this approach to enamel samples from Mission-Period ancestral Ohlone interred at Asistencia San Pedro y San Pablo (CA-SMA-71/H; n=11). For comparison, we also examine enamel from historic-period European-Americans interred in the City Cemetery in San Francisco, and extracted third molars from present-day military cadets. Results indicate that IgG is elevated among individuals at the asistencia relative to samples from present-day military cadets (n=8), or historic City Cemetery individuals (ANOVA with post-hoc Tukey Kramer tests, p < 0.02). Further, the inflammatory protein CRP, normally expressed at much lower levels than IgG, was present in 55% (6 of 11) of the asistencia samples, and in 17% (2 of 12) of the historic City Cemetery samples, but was not detected in enamel samples from contemporary military cadets. While more studies are needed, we argue that the difference in IgG could reflect higher levels of chronic diseases such as tuberculosis among Ohlone living within the Mission system, while the presence of measurable amounts of CRP could relate to high degrees of physical, social, and emotional stresses. To our knowledge, this is the first paleoproteomic study of immune proteins in tooth enamel. The ability to track immune responses during tooth formation could provide valuable and high-resolution information on ancient health and disease at the level of the individual over archaeological time-scales.

			Action	DRS
	Burialnumberandlabnumberconcordancefortoothenamel.txt	Txt
	QEPlus2_JY67.raw	Raw
	QEPlus2_JY68.raw	Raw
	QEPlus2_JY69.raw	Raw
	QEPlus2_JY70.raw	Raw