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Updated: Jun 26, 2026
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Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry
Published on: April 4, 2018
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Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines.
Michael Riffle, Alex Zelter, Daniel Jaschob
1Institute for Systems Biology, Seattle, Washington 98109, United States.
Journal of Proteome Research
|March 4, 2025
Summary
Limelight is a new, open-source tool for proteomics data visualization. It enables easy sharing, analysis, and interpretation of data-dependent acquisition (DDA) results from various software pipelines.
Area of Science:
- Proteomics
- Mass Spectrometry
- Bioinformatics
Background:
- Liquid chromatography-tandem mass spectrometry with data-dependent acquisition (DDA-LC-MS) is a key proteomics technique.
- Existing DDA data analysis tools often have limited visualization capabilities and are tied to specific software, hindering data sharing and interpretation.
- This fragmentation restricts the comparison of results across different DDA analysis pipelines.
Purpose of the Study:
- To develop an accessible, open-source tool for DDA-LC-MS data visualization and sharing.
- To create a platform independent of specific DDA search software pipelines.
- To facilitate the interpretation and comparison of proteomics data.
Main Methods:
- Development of Limelight, a user-friendly, open-source data visualization tool.
- Implementation of features for accessing and visualizing the entire data stack, from raw scans to identified proteins and modifications.
- Inclusion of data import tools compatible with various open-mass and closed-mass DDA search engine workflows.
Main Results:
- Limelight provides a unified platform for DDA-LC-MS data sharing, analysis, and visualization.
- The tool supports data from diverse DDA workflows and search engines.
- Users can access and interpret data, including peptide-spectrum matches and protein identifications, using native scores.
Conclusions:
- Limelight enhances the utility of DDA-LC-MS proteomics data by offering a flexible and collaborative visualization solution.
- The tool promotes data accessibility and reproducibility in proteomics research.
- Limelight supports comprehensive data interpretation, from raw spectral data to high-level protein and modification analysis.
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