Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform

Area of Science:

• Multi-omics research
• Proteomics
• Genomics

Background:

• Proteogenomics combines mass spectrometry-based proteomics with high-throughput sequencing.
• It aids in genomic annotation and identifies variant proteins from genomic variations like SNPs and Indels.
• Existing proteogenomic workflows involve complex, disparate software, hindering accessibility and reproducibility.

Purpose of the Study:

• To describe a user-friendly, reproducible proteogenomic analysis workflow.
• To leverage the Galaxy platform for integrated multi-omics data analysis.
• To facilitate the identification and classification of novel protein variants.

Main Methods:

• Development of an open-source, web-based Galaxy workflow for proteogenomic analysis.
• Creation of customized protein sequence databases.
• Matching spectral data against databases to identify peptide sequences and novel proteoforms.
• Variant classification and genomic visualization.

Main Results:

• The Galaxy workflow successfully integrates disparate software for proteogenomic analysis.
• It enables efficient matching of spectral data to customized databases.
• Novel protein variants are identified, classified, and visualized against the genome.
• The workflow enhances usability and reproducibility in proteogenomic studies.

Conclusions:

• The described Galaxy-based workflow simplifies complex proteogenomic analyses.
• It improves accessibility for researchers lacking extensive computational expertise.
• This approach enhances the reproducibility and efficiency of identifying and characterizing protein variants.