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IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry
Dmitry M Avtonomov1, Daniel A Polasky1, Brandon T Ruotolo1
1Department of Pathology, ‡Department of Chemistry, and §Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan United States.
New software, IMTBX and Grppr, enables automated analysis of complex top-down proteomics data from ion mobility mass spectrometry. This advances protein sequencing and post-translational modification analysis.
Area of Science:
- Proteomics
- Analytical Chemistry
- Biochemistry
Background:
- Top-down proteomics analyzes intact proteins for sequence and post-translational modifications (PTMs).
- Historically, this required ultrahigh resolution mass spectrometers due to spectral complexity.
- Advances now allow coupling ion mobility separation with faster, lower resolution mass analyzers.
Purpose of the Study:
- To address the lack of software for interpreting complex 2D spectra from ion mobility-coupled top-down experiments.
- To present a novel software suite for automated data processing.
Main Methods:
- Development of a software suite including IMTBX (IM Toolbox) and Grppr (Grouper).
- Application of the software to analyze intact proteins using a Waters Synapt G2 mass spectrometer with ion mobility.
- Comparison of automated analysis with previous manual and semi-automated methods.
Main Results:
- The software suite enables fully automated processing of 2D ion mobility-mass spectrometry data.
- Demonstrated capabilities in analyzing intact proteins.
- Validation against established data analysis procedures.
Conclusions:
- The presented software suite significantly enhances the analysis of top-down proteomics data.
- Automated processing of ion mobility-coupled top-down mass spectrometry data is now feasible.
- This facilitates more efficient and accessible protein characterization.
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