PXD016156 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD016156
- Label: PRIDE project
- Name: Proteomic Genotyping: Using Mass Spectrometry to Infer SNP Genotypes in Pigmented and Non-Pigmented Hair