IsoPepTracker: An interactive web application for peptide-driven isoform analysis.

Area of Science:

• Proteogenomics
• Molecular Biology
• Bioinformatics

Background:

• Alternative splicing impacts 95% of multi-exon genes, producing diverse protein isoforms.
• Current RNA-level analyses offer limited insight into protein-level changes.
• A gap exists in analyzing protein consequences of alternative splicing.

Purpose of the Study:

• To introduce IsoPepTracker, a web application for analyzing differential peptides across protein isoforms.
• To provide protein-level insights into alternative splicing events.
• To facilitate proteogenomics research by linking peptides to genes and isoforms.

Main Methods:

• Development of IsoPepTracker, a user-friendly web application with four modules: Canonical Isoform Analysis, Novel Isoform Discovery, Peptide Sequence Search, and Alternative Splicing Analysis.
• Integration of capabilities to analyze canonical and novel isoforms.
• Enabling analysis of peptides theoretically detectable by shotgun mass spectrometry.

Main Results:

• IsoPepTracker enables analysis and visualization of differential peptides related to alternative splicing.
• The application supports input of genes, novel cDNA sequences, peptides, or alternative splicing results.
• Case studies demonstrate the straightforward application of IsoPepTracker in proteogenomics.

Conclusions:

• IsoPepTracker provides informative peptide signatures to understand protein-level consequences of alternative splicing.
• The tool supplies peptide candidates for validation in shotgun proteomics experiments.
• IsoPepTracker bridges the gap between RNA-level splicing events and protein-level isoform diversity.