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Updated: Mar 8, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite
Caroline J DeHart1, Ryan T Fellers1, Luca Fornelli1
1Departments of Chemistry, Molecular Biosciences, the Proteomics Center of Excellence and the Robert H. Lurie Comprehensive Cancer Center at the Feinberg School of Medicine, Northwestern University, Evanston, IL, 60208, USA.
Top-down mass spectrometry analyzes intact proteins, offering a simpler approach than traditional methods. This study demonstrates using ProSight Lite software for analyzing these complex protein spectra to identify modifications.
Area of Science:
- Proteomics
- Mass Spectrometry
- Biochemistry
Background:
- Bottom-up proteomics fragments proteins into peptides, complicating analysis.
- Top-down proteomics analyzes intact proteins, offering direct characterization.
- Specialized software is required for processing top-down mass spectrometry data.
Purpose of the Study:
- To demonstrate the analysis of intact protein mass spectrometry data.
- To showcase the utility of ProSight Lite for top-down proteomics.
- To illustrate the characterization of proteoforms and post-translational modifications.
Main Methods:
- Analysis of intact protein fragmentation spectra.
- Utilizing deconvolution and deisotoping algorithms.
- Searching spectra with ProSight Lite, a free, vendor-agnostic software tool.
Main Results:
- Successful analysis of intact protein spectra was achieved.
- ProSight Lite facilitated the characterization of proteoforms.
- The software aided in discovering sites of post-translational modifications.
Conclusions:
- Top-down mass spectrometry, with tools like ProSight Lite, enables efficient protein characterization.
- This approach simplifies the analysis of complex proteoforms and modifications.
- ProSight Lite is a valuable, accessible tool for top-down proteomics research.
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