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Welcome to Limelight
=========================

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

Citing
===============
If you use Limelight in your work, please cite:

  .. epigraph::
   `Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines. Riffle M, Zelter A, Jaschob D, Hoopmann MR, Faivre DA, Moritz RL, Davis TN, MacCoss MJ, Isoherranen N. J Proteome Res. 2025 Apr 4;24(4):1895-1906. doi: 10.1021/acs.jproteome.4c00968. <https://pubmed.ncbi.nlm.nih.gov/40036265/>`_

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!

* Try using the `Limelight Issue Page at GitHub <https://github.com/yeastrc/limelight-core/issues>`_.
* You can `join our Slack <https://join.slack.com/t/limelight-ms/shared_invite/zt-pdkll4k3-YR5km0ppSrtdlZCJBvgVyQ>`_ and chat with us.
* You can email us at limelightms@uw.edu


Introduction
=============

**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 :ref:`Tutorials Page <Tutorials>`

.. toctree::
   :maxdepth: 2

   self
   using-limelight
   tutorials
   administration