PXD016156

PXD016156 is an original dataset announced via ProteomeXchange.

Title	Proteomic Genotyping: Using Mass Spectrometry to Infer SNP Genotypes in Pigmented and Non-Pigmented Hair
Description	Proteomic genotyping is the use of genetically variant peptides (GVPs), detected in a forensic protein sample, to infer the genotype of corresponding non-synonymous SNP alleles in the donor’s genome. This process does not depend on the presence of accessible or useable DNA in a sample. This makes proteomic genotyping an attractive alternative for analysis of problematic forensic samples, such as hair shafts, degraded bones or teeth, fingermarks, or sexual assault evidence. To demonstrate the concept in hair shafts, we developed an optimized sample processing protocol that could be used with high effectiveness on single hairs. This allows us to determine if the detected profiles of genetically variant peptides are robust and result in a consistent profile of inferred SNP alleles regardless of the chemical or biological history of the sample. Several real world scenarios have been evaluated. Here we include a study of four European subjects that had both pigmented and non-pigmented (or gray and non-gray) hair shafts. We tested whether (a) protein profiles change as a result of the loss of pigmentation and (b) these changes were reflected in the inferred genotype derived from detection of genetically variant peptides. Using this information, we can determine whether the resulting GVP profiles are more dependent on the biological context of pigmentation status or the underlying genotype.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:06:12.155.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 08:15:03	ID requested
1	2020-05-27 01:28:59	announced
⏵ 2	2024-10-22 05:06:12	announced	2024-10-22: Updated project metadata.

Franklin RN, Karim N, Goecker ZC, Durbin-Johnson BP, Rice RH, Parker GJ, Proteomic genotyping: Using mass spectrometry to infer SNP genotypes in pigmented and non-pigmented hair. Forensic Sci Int, 310():110200(2020) [pubmed]

10.1016/j.forsciint.2020.110200;

submitter keyword: Proteomic Genotyping, Hair, Hair Pigmentation, Melanosomes, Genetically Variant Peptides

Glendon John Parker
contact affiliation	University of California Davis
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/2020/05/PXD016156

PRIDE project URI

• PRIDE
  1. PXD016156
     1. Label: PRIDE project
     2. Name: Proteomic Genotyping: Using Mass Spectrometry to Infer SNP Genotypes in Pigmented and Non-Pigmented Hair