Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Optimization of Proteomics Sample Preparation for Forensic Analysis of Skin Samples

ABSTRACT: We present an efficient protein extraction and in-solution enzymatic digestion protocol optimized for mass spectrometry-based proteomics studies of human skin samples.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Skin

SUBMITTER: Maryam Baniasad

LAB HEAD: Michael Alan Freitas

PROVIDER: PXD022720 | Pride | 2021-11-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Optimization of proteomics sample preparation for forensic analysis of skin samples.

Baniasad Maryam M Reed Andrew J AJ Lai Stella M SM Zhang Liwen L Schulte Kathleen Q KQ Smith Alan R AR LeSassier Danielle S DS Weber Katharina L KL Hewitt F Curtis FC Woerner August E AE Gardner Myles W MW Wysocki Vicki H VH Freitas Michael A MA

Journal of proteomics 20210901

We present an efficient protein extraction and in-solution enzymatic digestion protocol optimized for mass spectrometry-based proteomics studies of human skin samples. Human skin cells are a proteinaceous matrix that can enable forensic identification of individuals. We performed a systematic optimization of proteomic sample preparation for a protein-based human forensic identification application. Digestion parameters, including incubation duration, temperature, and the type and concentration o ...[more]

PMID: 34481086

Similar Datasets

Proteomic Analysis of Protein in Human Fingerprints and Artificial Fingerprints

Project description:Quantitative genomic and proteomic evaluation of human latent fingerprint depositions represents a challenge within the forensic field, due to the high variability in the amount of DNA and protein initially deposited. To better assess recovery techniques for touch depositions, we present a method to produce simple and customizable artificial fingerprints. Capitalizing on recent advancements in the use of protein sequence identification for human forensic analysis, these samples contain a representative quantity of protein, originating from epidermal skin cells collected from the fingers and palms of volunteers. Proteomic sequencing by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis indicates a high level of protein overlap between artificial and latent prints.

2019-09-26 | PXD015445 | Pride

Novel biallelic mutations in POLR1A: expansion of the phenotype and insight into the molecular mechanism

Project description:The eukaryotic genome is transcribed by three RNA polymerases (Pol) I, II and III; each transcribing different classes of RNAs. Pol I transcribes ribosomal DNA and produces the polycistronic rRNA 47S, which releases 28S, 18S and 5.8S rRNAs. Heterozygous mutations in the Pol I subunit POLR1A have been described in three patients presenting with Acrofacial Dysostosis, Cincinnati Type (MIM 616462), while a homozygous mutation in POLR1A was identified in two siblings, presenting developmental regression and several brain anomalies. We present three patients with homozygous mutations in POLR1A. Patient 1, a Norwegian male homozygous for POLR1A p.T642N, presented severe neurodegeneration with epilepsy, and died at 16 years of age. Patient 2, a 5.4-years-old Mexican male homozygous for POLR1A p.R667H, presented with severe neurodegeneration, epilepsy, and skeletal anomalies. Patient 3, a 2-year-old Dutch girl homozygous for POLR1A p.T642N, manifested severe global developmental delay, and brain anomalies. Structure superimposition of POLR1A wild-type and POLR1A T642N or R667H suggested a possible abnormal interaction between POLR1A and POLR2H. In vitro experiments showed that POLR1A T642N has higher transcriptional activity, abnormal rRNA processing, increased autophagy, deprotected telomeres, and reduced levels of p53. Proteomics analysis of patients 1 supported these findings, identifying dysfunction of pathways related to protein synthesis, ubiquitination, phagosome activities, and cell survival. In conclusion, we expand the phenotype of this rare disease and document a transcriptional defect affecting multiple processes, which impact cell survival.

2023-10-24 | PXD017431 | Pride

Serial mixture of peptides from mouse skin and primary human mesenchymal stem cells for protein quant methods benchmarking

Project description:Multivariate regression modelling provides a statistically powerful means of quantifying the effects of a given treatment while compensating for sources of variation and noise, such as variability between human donors and the behaviour of different peptides during mass spectrometry. However, methods to quantify endogenous post-translational modifications (PTMs) are typically reliant on summary statistical methods that fail to consider sources of variability such as changes in levels of the parent protein. Here, we compare three multivariate regression methods, including a novel Bayesian elastic net algorithm (BayesENproteomics) that enables assessment of relative protein abundances while also quantifying identified PTMs for each protein. We tested the ability of these methods to accurately quantify expression of proteins in a mixed-species benchmark experiment, and to quantify synthetic PTMs induced by stable isotope labelling. Finally, we extended our regression pipeline to calculate fold changes at the pathway level, providing a complement to commonly used enrichment analysis. Our results show that BayesENproteomics can quantify changes to protein levels across a broad dynamic range while also accurately quantifying PTM and pathway-level fold changes.

2019-03-12 | PXD012772 | Pride

Biomarker discovery for ectoparasite host resistance in cattle

Project description:This project aimed to discover the protein-based biomarkers for tick resistance in cattle using cattle skin samples. The cattle were phenotyped into two groups, tick-resistant and susceptible after artificial tick challenge. Mean tick scores were used to categorise cattle. The SWATH analysis was sued to measure the relative abundance of proteins in skin samples of the two groups at different time points.

2023-01-25 | PXD036561 | Pride

The Transglutaminase-2 interactome in the APP23 mouse model of Alzheimer disease

Project description:Amyloid-beta (Aβ) deposition in the brain, is closely linked to development of Alzheimer’s disease (AD). Unfortunately, therapies specifically targeting Aβ deposition have failed to reach their primary clinical endpoints, emphasizing the need to broaden the search strategy for identification of alternative therapeutic targets/mechanisms. Transglutaminase (TG2) catalyses posttranslational modifications, is present in characteristic AD lesions and has AD-associated proteins, including Aβ, tau and apolipoprotein E. However, an unbiased overview of TG2 interactors (TG2 interactome) and the cellular pathways of which these interactors are part in control and AD brain is lacking. Here, anticipating future studies in AD brain, we aimed to identify these interactors and their pathways using a crossbred of the AD-mimicking APP23 mouse model with wildtype and TG2-/- mice. We found that absence of TG2 had no (statistically) significant effect on Aβ pathology, soluble brain levels of Aβ1-40, Aβ1-42, and mRNA levels of TG2 family members compared to APP23 mice. Quantitative proteomics and network analysis revealed a large cluster of TG2 interactors with synaptic transmission/assembly and cell adhesion typical of AD in the APP23 brain. Comparative proteomics were in line with these observations as it also revealed association of proteins of both pathways to be linked to TG2 in APP23 brains Together, our data showed that TG2 deletion led to considerable network alterations consistent with a role of TG2 in (dys)regulation of synaptic transmission and cell adhesion in APP23 brains.

2022-02-22 | PXD030354 | Pride

Mouse skin technical replicate negative control

2019-03-12 | PXD012784 | Pride

Species identification of archaeological skin objects from Danish bogs

Project description:Denmark has an extraordinarily large and well-preserved collection of archaeological skin garments found in peat bogs, dated to approximately 920 BC - AD 775. These objects provide not only the possibility to study prehistoric skin costume and technologies, but also to investigate the animal species used for production of skin garments. Until recently, species identification of archaeological skin was mainly performed by light and scanning electron microscopy or analysis of ancient DNA. However, the efficacy of these methods can be limited due to the harsh, mostly acidic environment of peat bogs leading to morphological and molecular degradation within the samples. We compared species assignment results of twelve archaeological skin samples from Danish bogs using Mass Spectrometry (MS)-based peptide sequencing, against results obtained using light and scanning electron microscopy

2014-07-29 | PXD001029 | Pride

Transcription profiling of S. cerevisiae mre11, rad50 and spo11 mutants in premeiosis and meiotic prophase

Project description:Mre11, together with Rad50 and Xrs2/NBS, plays pivotal roles in homologous recombination, repair of DNA double strand breaks (DSBs), activation of damage-induced checkpoint, and telomere maintenance. Using DNA microarray assays to analyze yeast mutants (mre11delta, rad50delta, and spo11Y135F) defective for meiotic DSB formation, we demonstrate that the absence of Mre11 in yeast causes specific effects on regulation of a class of meiotic genes for spore development. The transcriptional deficiency was not observed in other DSB mutants such as rad50delta and spo11Y135F, suggesting the transcriptional defect in mre11delta is due to neither lack of meiotic DSB formation, nor disintegrity of Mre11-Rad50-Xrs2 complex.These defects were confirmed by northern and lacZ reporter gene assays. Experiment Overall Design: Gene expression data from wild type, mre11delta, rad50delta, and spo11Y135F cells in premeiosis (meiosis 0 hr) and prophase (meiosis 4 hr). Affymetrix GeneChip YG-S98 was used. All strains used were SK1 background diploid cells.

2007-10-23 | E-GEOD-6620 | biostudies-arrayexpress

Cardiac miRNA expression changes induced by prediabetes

Project description:The aim of the experiment was the analysis of key molecular changes with an unbiased, transcriptomics-based approach in a prediabetes model. Small RNA sequencing analysis was applied to explore the expression changes resulted high-fat chow (supplemented with 40% lard) diet for 21 weeks and a single low dose of streptozotocin (20 mg/kg) treatment at week 4. Long-Evans rats were used in the present study. Left ventricular samples(n=6) of both prediabetic and control groups were analyzed.

2020-04-24 | E-MTAB-8204 | biostudies-arrayexpress

COL1 database samples for the Late Pleistocene of Western Eurasia

Project description:The project aimed to characterize the collagen type I (COL1) sequences from various modern, Holocene and Pleistocene bone, antler and skin samples for phylogenetic purposes. All extractions were performed at BioArCh, University of York (UK) or the Department of Human Evolution, MPI-EVA (Germany). Analyses took place on Q-Exactive Hybrid Quadrupole-Orbitrap MS.

2016-09-27 | PXD003190 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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