Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry

Area of Science:

• Proteomics
• Genomics
• Bioinformatics

Background:

• Proteogenomic studies integrate genomic and transcriptomic data with mass spectrometry for proteoform identification.
• Current research primarily uses bottom-up mass spectrometry, with limited adoption of top-down approaches.
• A lack of specialized software hinders top-down proteogenomic data analysis.

Purpose of the Study:

• To develop a computational tool, TopPG, for generating proteoform sequence databases.
• To facilitate the analysis of top-down proteogenomic data, incorporating genetic alterations and alternative splicing.
• To enable the identification of proteoforms with sample-specific variants.

Main Methods:

• Development of TopPG software for database generation.
• Application of TopPG to analyze top-down mass spectrometry data from DLD-1 colorectal cancer cells.
• Integration of genomic and transcriptomic data with top-down mass spectrometry results.

Main Results:

• TopPG successfully generated proteoform sequence databases incorporating genetic alterations and alternative splicing.
• The tool enabled confident identification of proteoforms with sample-specific alterations in colorectal cancer cells.
• Demonstrated the utility of TopPG in a real-world top-down proteogenomic study.

Conclusions:

• TopPG is an effective tool for top-down proteogenomic data analysis.
• The software aids in identifying complex proteoforms, including those with sample-specific variants.
• TopPG addresses the need for specialized tools in the growing field of top-down proteogenomics.