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Finding haplotypic ...
Finding haplotypic signatures in proteins
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- Vasicek, Jakub (författare)
- Univ Bergen, Dept Clin Sci, Mohn Ctr Diabet Precis Med, N-5021 Bergen, Norway.;Univ Bergen, Dept Informat, Computat Biol Unit, N-5008 Bergen, Norway.
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- Skiadopoulou, Dafni (författare)
- Univ Bergen, Dept Clin Sci, Mohn Ctr Diabet Precis Med, N-5021 Bergen, Norway.;Univ Bergen, Dept Informat, Computat Biol Unit, N-5008 Bergen, Norway.
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- Kuznetsova, Ksenia G. . (författare)
- Univ Bergen, Dept Clin Sci, Mohn Ctr Diabet Precis Med, N-5021 Bergen, Norway.;Univ Bergen, Dept Informat, Computat Biol Unit, N-5008 Bergen, Norway.
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- Wen, Bo (författare)
- Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA.
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- Johansson, Stefan (författare)
- Univ Bergen, Dept Clin Sci, Mohn Ctr Diabet Precis Med, N-5021 Bergen, Norway.;Haukeland Hosp, Dept Med Genet, N-5021 Bergen, Norway.
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- Njolstad, Pal R. (författare)
- Univ Bergen, Dept Clin Sci, Mohn Ctr Diabet Precis Med, N-5021 Bergen, Norway.;Haukeland Hosp, Children & Youth Clin, N-5021 Bergen, Norway.
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- Bruckner, Stefan (författare)
- Univ Rostock, Inst Visual & Analyt Comp, Chair Visual Analyt, D-18051 Rostock, Germany.
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- Käll, Lukas, 1969- (författare)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Vaudel, Marc (författare)
- Univ Bergen, Dept Clin Sci, Mohn Ctr Diabet Precis Med, N-5021 Bergen, Norway.;Univ Bergen, Dept Informat, Computat Biol Unit, N-5008 Bergen, Norway.;Norwegian Inst Publ Hlth, Dept Genet & Bioinformat Hlth Data & Digitalizat, N-0473 Oslo, Norway.
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Univ Bergen, Dept Clin Sci, Mohn Ctr Diabet Precis Med, N-5021 Bergen, Norway;Univ Bergen, Dept Informat, Computat Biol Unit, N-5008 Bergen, Norway. Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA. (creator_code:org_t)
- Oxford University Press (OUP), 2023
- 2023
- Engelska.
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Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 12
- Relaterad länk:
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https://doi.org/10.1...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Background: The nonrandom distribution of alleles of common genomic variants produces haplotypes, which are fundamental in medical and population genetic studies. Consequently, protein-coding genes with different co-occurring sets of alleles can encode different amino acid sequences: protein haplotypes. These protein haplotypes are present in biological samples and detectable by mass spectrometry, but they are not accounted for in proteomic searches. Consequently, the impact of haplotypic variation on the results of proteomic searches and the discoverability of peptides specific to haplotypes remain unknown. Findings: Here, we study how common genetic haplotypes influence the proteomic search space and investigate the possibility to match peptides containing multiple amino acid substitutions to a publicly available data set of mass spectra. We found that for 12.42% of the discoverable amino acid substitutions encoded by common haplotypes, 2 or more substitutions may co-occur in the same peptide after tryptic digestion of the protein haplotypes. We identified 352 spectra that matched to such multivariant peptides, and out of the 4,582 amino acid substitutions identified, 6.37% were covered by multivariant peptides. However, the evaluation of the reliability of these matches remains challenging, suggesting that refined error rate estimation procedures are needed for such complex proteomic searches. Conclusions: As these procedures become available and the ability to analyze protein haplotypes increases, we anticipate that proteomics will provide new information on the consequences of common variation, across tissues and time.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Nyckelord
- proteogenomics
- haplotype
- protein
- bioinformatics
- post-translational modification
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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Vasicek, Jakub
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Skiadopoulou, Da ...
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Kuznetsova, Ksen ...
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Wen, Bo
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Johansson, Stefa ...
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Njolstad, Pal R.
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Bruckner, Stefan
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Käll, Lukas, 196 ...
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Vaudel, Marc
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