PXD016155

PXD016155 is an original dataset announced via ProteomeXchange.

Title	Optimal Processing for Proteomic Genotyping of Single Human Hairs
Description	The human hair proteome offers new insight in the field of human identification. Hair often contains DNA that has been degraded due to the process of cornification. The smaller fragments of DNA present a challenge for obtaining useful information concerning the identity of the donor. Proteomic genotyping offers an alternative approach which starts with protein, a biomolecule abundant in the hair shaft. Nonsynonymous single nucleotide polymorphisms may be detected in the sequence of these proteins, allowing the inference of SNP genotypes. Population genetics-based information from these genotypes may be used to calculate random match probability or even infer ancestry. The current challenge of this research is to optimize processing chemistry in order to maximize genetic information from a single human hair shaft. Results indicate that optimal conditions for proteomic analysis of a single human hair include 6 hrs of reduction with 100 mM dithiothreitol at room temperature, alkylation with 200 mM iodoacetamide for 45 min, and 6 hrs of digestion with two 1:50 (enzyme:protein) additions of stabilized trypsin at room temperature, with stirring incorporated into all three steps. Our final conditions using optimized temperatures and incubation times for disulfide reduction and protein digestion produced random match probabilities of up to 1 in 624 million from a single hair with a median value of 1 in 1.1 million, compared to a maximum random match probability of 1 in 1380 and a median value of 1 in 24 for the original processing method.
HostingRepository	PRIDE
AnnounceDate	2020-06-10
AnnouncementXML	Submission_2020-06-10_05:44:37.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Glendon Parker
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-05 08:14:42	ID requested
⏵ 1	2020-06-10 05:44:38	announced

Goecker ZC, Salemi MR, Karim N, Phinney BS, Rice RH, Parker GJ, Optimal processing for proteomic genotyping of single human hairs. Forensic Sci Int Genet, 47():102314(2020) [pubmed]

submitter keyword: Forensic science, hair, proteomic genotyping, sample processing, genetically variant peptides

Glendon John Parker
contact affiliation	Department of Environmental Toxicology, University of California, Davis, USA
contact email	gjparker@ucdavis.edu
lab head
Glendon Parker
contact affiliation	UC Davis
contact email	gjparker@ucdavis.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/06/PXD016155

PRIDE project URI

• PRIDE
  1. PXD016155
     1. Label: PRIDE project
     2. Name: Optimal Processing for Proteomic Genotyping of Single Human Hairs