ProHap Explorer: Visualizing Haplotypes in Proteogenomic Datasets Article Swipe

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Jakub Vašíček , Dafni Skiadopoulou , Ksenia G. Kuznetsova , Lukas Käll , Marc Vaudel , Stefan Brückner ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.48550/arxiv.2504.06282

In mass spectrometry-based proteomics, experts usually project data onto a single set of reference sequences, overlooking the influence of common haplotypes (combinations of genetic variants inherited together from a parent). We recently introduced ProHap, a tool for generating customized protein haplotype databases. Here, we present ProHap Explorer, a visualization interface designed to investigate the influence of common haplotypes on the human proteome. It enables users to explore haplotypes, their effects on protein sequences, and the identification of non-canonical peptides in public mass spectrometry datasets. The design builds on well-established representations in biological sequence analysis, ensuring familiarity for domain experts while integrating novel interactive elements tailored to proteogenomic data exploration. User interviews with proteomics experts confirmed the tool's utility, highlighting its ability to reveal whether haplotypes affect proteins of interest. By facilitating the intuitive exploration of proteogenomic variation, ProHap Explorer supports research in personalized medicine and the development of targeted therapies.

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Type: preprint
Language: en
Landing Page: http://arxiv.org/abs/2504.06282
PDF: https://arxiv.org/pdf/2504.06282
OA Status: green
OpenAlex ID: https://openalex.org/W4417239951

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OpenAlex ID: https://openalex.org/W4417239951

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DOI: https://doi.org/10.48550/arxiv.2504.06282

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Title: ProHap Explorer: Visualizing Haplotypes in Proteogenomic Datasets

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Type: preprint

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Language: en

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Publication year: 2025

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Publication date: 2025-03-25

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Authors: Jakub Vašíček, Dafni Skiadopoulou, Ksenia G. Kuznetsova, Lukas Käll, Marc Vaudel, Stefan Brückner

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Landing page: https://arxiv.org/abs/2504.06282

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PDF URL: https://arxiv.org/pdf/2504.06282

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Cited by: 0

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