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Part II: Proteomics Target Approach for Taxonomic and Sex Identification in Modern and Archaeological Enamel Caprines

ABSTRACT: In this study, we applied proteomic analytical methods to modern caprine (sheep, Ovis aries and goat, Capra hircus) tooth enamel to establish a reliable method for identifying species-specific and sex-specific peptides. Utilizing single amino acid variations (SAAVs) in Enamelin (Enam) and Amelogenin (Amel) proteins, we developed a targeted parallel reaction monitoring (PRM) assay to identify molecular markers preserved in enamel of modern caprines.

INSTRUMENT(S):

ORGANISM(S): Capra Hircus (goat)

TISSUE(S): Enamel Organ, Enamel

SUBMITTER: Paula Kotli

LAB HEAD: Prof. Elisabetta Boaretto

PROVIDER: PXD058279 | Pride | 2025-09-15

REPOSITORIES: Pride

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			Action	DRS
	FS1_EB_22316_431_03092024.raw_20240930_Amel.mgf	Mgf
	FS1_EB_22316_431_03092024.raw_20240930_Amel.mzid.gz	Mzid
	FS1_EB_22316_431_03092024.raw_20240930_Enam.mgf	Mgf
	FS1_EB_22316_431_03092024.raw_20240930_Enam.mzid.gz	Mzid
	FS1_EB_22316_432_03092024.raw_20240930_Amel.mgf	Mgf

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Publications

Sex Identification and Species Confirmation in Modern and Archeological Caprine Enamel.

Kotli Paula P Morgenstern David D Ben-Dor Shifra S Kolska Horwitz Liora L Boaretto Elisabetta E

Journal of proteome research 20250806 9

Proteomics has become a transformative tool for species and sex determination. This study introduces a novel methodology that integrates amelogenin (Amel) and enamelin (Enam) proteins extracted from the tooth enamel of caprines. Since morphologically, osteological remains of sheep and goats often cannot be easily discriminated, we developed our method on both modern domestic sheep (<i>Ovis aries</i>) and goats (<i>Capra hircus</i>) to establish unique proteomic signatures for each species for se ...[more]

PMID: 40768595

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Part I: Proteomics Target Approach for Taxonomic and Sex Identification in Modern and Archaeological Enamel Caprines

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2025-09-15 | PXD058275 | Pride

Label-Free Quantification Method for Assessing Sex from Modern and Ancient Bovine Tooth Enamel. PART III

Project description:Identification of the sex of modern, fossil and archaeological animal remains offers many insights into their demography, mortality profiles and domestication pathways. However, due to manifold factors, sex determination of such remains is often impossible. To overcome this, we have developed an innovative protocol to determine an animal sex applying label-free quantification (LFQ) of two unique AmelY peptides ‘LRYPYP’ (AmelY;[M+2]2+ 404.7212 m/z) and ‘LRYPYPSY’ (AmelY;[M+2]2+ 529.7689 m/z) that are solely present in tooth enamel of males. we applied this method to eight (8) modern cattle (Bos taurus) and (12) twelve archaeological samples of Bos from a Neolithic sites of Beisamoun, Israel (8th–7th millennium BC). Our methodology correctly identified the sex of the modern samples and enabled determination of sex in the archaeological samples.

2024-10-17 | PXD053225 | Pride

Label-Free Quantification Method for Assessing Sex from Modern and Ancient Bovine Tooth Enamel PART II

Project description:Identification of the sex of fossil and archaeological animal remains offers many insights into their demography, mortality profiles and domestication pathways. However, due to manifold factors, sex determination of fossils is often impossible. To overcome this, we have developed an innovative protocol to determine animal’s sex applying label-free quantification (LFQ) of two unique AmelY peptides ‘LRYPYP’ (AmelY;[M+2]2+ 404.7212 m/z) and ‘LRYPYPSY’ (AmelY;[M+2]2+ 529.7689 m/z) that are solely present in males that permitted determination of the animal’s sex. We examine the application of this method to eight (8) modern cattle (Bos taurus) and (12) twelve fossil (Bos) samples from a Neolithic sites of Beisamoun in Israel (8th–7th millennium BC). Our methodology correctly determinate sex in all modern and ancient samples.

2024-10-17 | PXD053148 | Pride

Automated high-throughput biological sex identification from archaeological human dental enamel using targeted proteomics

Project description:Biological sex is a key information for archaeological and forensic studies, which can be assessed in enamel using proteomics. However, the lack of a standard approach for fast and accurate sex identification limits the reach of proteomics applications. Here, we introduce a targeted proteomics-based workflow that builds on a rapid, non-destructive, sensitive, and quantitative mass spectrometry (MS) strategy for the determination of biological sex from human dental enamel, including a R-Shiny interface for the data analysis. The method was first developed and optimised using modern teeth material and then validated on an independent set of modern deciduous teeth of known sex. The assay was then applied to archaeological material and demonstrated unprecedented specificity and scalability for molecular sex inference, with the possibility of analysing > 300 individuals in less than two days of MS measurement time, and with subsequent confident sex assignment in less than a day of data analysis.

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Label-Free Quantification Method for Assessing Sex from Modern and Ancient Bovine Tooth Enamel

2024-10-17 | PXD053146 | Pride

Anti-SARS-CoV-2 antibodies elicited by COVID-19mRNA vaccine exhibits a unique glycosylation pattern

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2021-11-29 | PXD029321 | Pride

Site- and structure-specific glycosylation signatures of bovine, caprine, porcine and human milk-derived extracellular vesicles

Project description:Intact glycopeptides in MEVs from bovines, caprines, porcines and humans were comprehensively analyzed by high-resolution mass spectrometry using the sceHCD followed by EThcD fragment method, revealing that protein glycosylation is abundant and heterogeneous in MEVs.

2024-01-30 | PXD044641 | Pride

Fresh insights into sex-specific mobility in Copper Age Perdigões (Reguengos de Monsaraz, Portugal) provided by amelogenin peptide analysis

Project description:Sex determination through amelogenin peptides from dental enamel has, in recent years, opened new possibilities to the study of prehistoric demography. Although this technique can be used on teeth of any chronology, it bears especial significance for the analysis of prehistoric collective burials, where bone remains often appear commingled and disarticulated, which makes sexual determination extremely difficult or even impossible. Traditionally, the impossibility to sex buried subjects has prevented making assessments in social or demographic terms for which gender was a key aspect, including mobility, diet, social inequality or ancestry, among others. In this paper, sex data of 34 individuals from the Late Neolithic-Chalcolithic site of Perdigões (Reguengos de Monsaraz, Portugal) obtained through amelogenin peptides analysis of dental enamel are presented. This new evidence is of great relevance at a site in which the large majority of the vast collection of human remains discovered so far (MNI = 551) are heavily commingled and highly fragmented. Interpretation of the results proceeds at two levels: i) firstly we consider the chronological and spatial distribution of the funerary structures: ii) secondly, we look into the Sr values available for each of them. The results show a greater number of male (n=6) than female (n=2) individuals among local subjects, and a balance between men (n=13) and women (n=13) for non-local ones, suggesting similar residential mobility for both sexes. These results are assessed within the context of the evidence available both for the Iberian Peninsula and the European continent. The greater female mobility observed at sites with similar chronologies in Central Europe, which has been interpreted in terms of female exogamy and patrilocality, is not replicated at Perdigões, where men and women present similar values.

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