Welcome to Limelight

Limelight is a web application for analyzing, visualizing, and sharing and bottom-up proteomics results.


If you use Limelight in your work, please cite:

Getting Help, Providing Feedback, or Reporting Problems

If after reading this documentation you have questions about Limelight, ideas for new features, or want to report any problems, please contact us!


Limelight is designed to provide you with the full-stack of proteomics results, regardless of which processing pipeline you used to search your data. Full-stack means that you have access to the global views of your data (such as statistically comparing conditions), to viewing lists of proteins and peptides, to individual PSMs and spectra–all showing the native scores from whichever pipeline you used. Additionally, all native scores from your pipeline are available to you for filtering–even when contrasting multiple searches that each used different pipelines.

Tutorials for Running Pipeline

We have developed tutorials to accompany Riffle M, Hoopmann M, et al. (2022) that describe the process for running the Magnum, Percolator, Limelight pipeline; and how to then perform the statistical test for finding mods of interest in Limelight. Please see our Tutorials Page