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PXD016156

PXD016156 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProteomic Genotyping: Using Mass Spectrometry to Infer SNP Genotypes in Pigmented and Non-Pigmented Hair
DescriptionProteomic 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:06:12.155.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterGlendon Parker
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-11-05 08:15:03ID requested
12020-05-27 01:28:59announced
22024-10-22 05:06:12announced2024-10-22: Updated project metadata.
Publication List
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;
Keyword List
submitter keyword: Proteomic Genotyping, Hair, Hair Pigmentation, Melanosomes, Genetically Variant Peptides
Contact List
Glendon John Parker
contact affiliationUniversity of California Davis
contact emailgjparker@ucdavis.edu
lab head
Glendon Parker
contact affiliationUC Davis
contact emailgjparker@ucdavis.edu
dataset submitter
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Dataset FTP location
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PRIDE project URI
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