Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SPEED-E: A modified version of the Sample Preparation by Easy Extraction and Digestion(-free) protocol for Enamel-based sex determination

ABSTRACT: Development of the Sample Preparation by Easy Extraction and Digestion-free for Enamel (SPEED-E) for sex determination of human remains. Applied to 88 subadult and juvenile individuals from the First Baptist Church of Philadelphia assemblage of human skeletal remains from Philadelphia, Pennsylvania, USA.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Timothy Cleland

PROVIDER: MSV000093535 | MassIVE | Wed Nov 29 08:14:00 GMT 2023

SECONDARY ACCESSION(S): PXD047380

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Sex determination of human remains from peptides in tooth enamel

Project description:Biological sex determination of human remains by means of a minimally destructive surface acid etch of tooth enamel and subsequent identification of sex chromosome linked isoforms of Amelogenin– an enamel-forming protein - by nano-liquid chromatography mass spectrometry(nanoLC-MS).

2017-12-12 | PXD007856 | Pride

Sex Determination of Infant Remains

Project description:This study tests the application of an innovative new method of sex determination utilizing enamel peptides on a sample of incompletely developed deciduous teeth, including those of perinates.

2021-01-28 | PXD021683 | Pride

Rapid amelogenin sex estimation using untargeted Evosep-timsTOF mass spectrometry

Project description:Data dependent acquisition of enamel proteins, focussed on amelogenins, for sex estimation of archaeological remains

2024-08-06 | MSV000095527 | MassIVE

Sex determination of archaeological samples using peptide analysis of amelogenin

Project description:We have extended the sample handling and data analysis methods used to determine sex from archaeological fragments of teeth. The dental enamel protein amelogenin is isomorphic based on sex; we quantify the expression of peptide fragments of AMELX and AMELY using MS2 proteomics.

2020-04-13 | MSV000085277 | MassIVE

Sex estimation of human remains using the results of tooth enamel peptidomic analyses, LC-MSMS

Project description:Sex of individuals, estimated on human remains, is important information in anthropological, archaeological and forensic researches. In forensic anthropology, this is one of the key points for identifying a person. In archeology and paleoanthropology, information about sex is important for reconstructing the social and biological structure of a group, lifestyle, and for modeling demographic and growth processes in the past. Sex estimation of adult individuals is possible according to morphological criteria when metric and descriptive features are used. In case of poor preservation of the adult skeletons, as well as on children's remains, sex estimation by morphological criteria has some limitations. Therefore regular attempts are made to attract alternative methods for sexing human remains. As one of such methods a liquid chromatography-mass spectrometry analysis of tooth enamel peptides can be used. The result of this analysis is the identification of certain fragments of amelogenins - the main structural proteins of the organic matrix of tooth enamel, which make up more than 90% of its protein content. Amelogenin genes are located on both the X- and Y-chromosomes and the products of these genes have structural differences that allow them to be differentiated from each other. In the process of maturation of tooth enamel, its protein matrix undergoes proteolytic degradation, as a result enamel already contains proteins in the form of their peptide fragments. Reliable and reproducible detection of unique peptide fragments of amelogenins encoded on the X- and Y-chromosomes in human enamel will make it possible to estimate sex of human remains. The work presents a peptidomic analysis of tooth enamel using chromatography-mass spectrometry. Experiments were carried out on a series of teeth of various archaeological data, tafonomic condition of crown and different biological generations of teeth (deciduous and permanent ones).

2020-06-24 | PXD017965 | Pride

Systematic evaluation of RNA-Seq preparation protocol performance

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-06-27 | GSE131398 | GEO

Moth sex determination

Project description:Sex determination in the flour moth, Ephestia kuehniella.

| PRJEB45597 | ENA

Modified PCR protocol to increase sensitivity for determination of bacterial community composition.

Project description:BackgroundThe objective of this project was to increase the sensitivity of sequence-based bacterial community determination without impacting community composition or interfering with cluster formation during sequencing. Two PCR protocols (standard and modified) were examined in airway samples where we observed a large range in bacterial load (3.1-6.2 log10 16S rRNA gene copies/reaction). Tracheal aspirate (TA) samples (n = 99) were collected from sixteen children requiring mechanical ventilation at a single center. DNA was extracted, and total bacterial load (TBL) was assessed using qPCR. Amplification of 16S rRNA was attempted with both protocols in all samples.ResultsPCR product was observed using both protocols in 52 samples and in 24 additional samples only with the modified protocol. TBL, diversity metrics, and prominent taxa were compared for samples in three groups based on success of the two protocols (successful with both, success with modified only, unsuccessful for both). TBL differed significantly across the three groups (p<0.001). Specifically, the modified protocol allowed amplification from samples with intermediate TBL. Shannon diversity was similar between the two protocols, and Morisita-Horn beta diversity index showed high agreement between the two protocols within samples (median value 0.9997, range 0.9947 to 1). We show that both protocols identify similar communities, and the technical variability of both protocols was very low. The use of limited PCR cycles was a key feature to limit impact of background by exclusion of 24% of samples with no evidence of bacterial DNA present in the sample.ConclusionThe modified amplification protocol represents a viable approach that increased sensitivity of bacterial community analysis, which is important for study of the human airway microbiome where bacterial load is highly variable. Video abstract.

| S-EPMC8045227 | biostudies-literature

Proteomic sex determination vs osteological sex estimation – what effect do our techniques have on the way we view the people of the past?

Project description:Amelogenin, a protein involved in the formation of enamel occurs as two isoforms, AMEL X and AMEL Y, which are encoded on the X and Y chromosome respectively. Isoform-specific peptides can be used for the determination of the chromosomal sex in ancient teeth. This strategy was used to determine the chromosomal sex of individuals from tooth material of historic New Zealand cemetery samples by mass spectrometry-based amelogenin peptide analysis. We show what can happen when osteobiographies are constructed for individuals for whom osteological sex estimation was inaccurate. We also highlight the uses of peptide analysis in identifying individuals, particularly non-adults for whom osteological sex estimation is not possible. Peptide analysis of historic New Zealand cemetery samples has helped to change our interpretations and added to our understanding of these populations.

2025-11-25 | PXD066946 | Pride

Sex Estimation Using Sexually Dimorphic Amelogenin Protein Fragments in Human Enamel

Project description:Sex estimation of human remains from demineralized blocks of tooth enamel by liquid chromatography tandem mass spectrometry (LC- MS/MS) and proteomic analysis of sexually dimorphic amelogenin peptides. The detection of the Y-isoform of amelogenin is used to estimate male sex. The combined signal intensity of the sexually dimorphic peptides from each samples of known sex is used to establish a statistical framework for the estimation of the female sex probability.

2018-11-29 | PXD009781 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data