ProHap Explorer: Visualizing Haplotypes in Proteogenomic Datasets

Area of Science:

• Proteomics
• Genomics
• Bioinformatics

Background:

• Mass spectrometry-based proteomics typically uses single reference sequences, ignoring haplotype influences.
• Haplotypes, combinations of inherited genetic variants, can alter protein sequences and their detection.
• Existing tools do not adequately visualize the impact of common haplotypes on proteomic data.

Purpose of the Study:

• To introduce ProHap Explorer, a novel visualization interface for exploring haplotype effects on the human proteome.
• To enable users to investigate how common haplotypes influence protein sequences and identify non-canonical peptides.
• To support the analysis of proteogenomic variation in mass spectrometry datasets.

Main Methods:

• Development of ProHap Explorer, a user-friendly interface for visualizing proteogenomic data.
• Integration of established biological sequence analysis representations with interactive elements.
• Testing and validation through user interviews with proteomics experts.

Main Results:

• ProHap Explorer facilitates the exploration of haplotypes and their impact on protein sequences.
• The tool aids in identifying non-canonical peptides in public mass spectrometry datasets.
• User feedback confirmed the utility of ProHap Explorer in assessing haplotype effects on proteins of interest.

Conclusions:

• ProHap Explorer provides an intuitive platform for exploring proteogenomic variation.
• The tool enhances the understanding of haplotype influences in mass spectrometry-based proteomics.
• ProHap Explorer supports advancements in personalized medicine and targeted therapy development.