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ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment
Diogo B Lima1, Mathieu Dupré1, Magalie Duchateau1
1Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France.
Bioinformatics (Oxford, England)
|November 9, 2020
Summary
ProteoCombiner integrates shotgun and top-down proteomic data for enhanced proteoform analysis. This software aids in visualizing, validating, and comparing proteoform sequences and post-translational modifications.
Area of Science:
- Proteomics
- Computational Biology
- Bioinformatics
Background:
- Proteomic data analysis often involves integrating diverse datasets from different experimental approaches.
- Identifying and characterizing proteoforms, including post-translational modifications (PTMs), presents significant computational challenges.
Purpose of the Study:
- To develop a high-performance software tool for integrating shotgun and top-down proteomic data.
- To facilitate the rapid visualization, manual validation, and comparison of identified proteoform sequences and their PTMs.
Main Methods:
- Development of ProteoCombiner software.
- Integration of data from multiple experiments and search engines.
- Application to a large-scale Escherichia coli dataset.
Main Results:
- ProteoCombiner effectively integrates shotgun and top-down proteomic data.
- The software enables efficient visualization and validation of proteoforms.
- Demonstrated unambiguous proteoform identification and characterization on an E. coli dataset.
Conclusions:
- ProteoCombiner provides a robust solution for comprehensive proteoform analysis.
- The tool enhances the accuracy and efficiency of proteomic data interpretation.
- Facilitates the study of proteome complexity and PTMs.
