MassDash
========

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Welcome to MassDash Documentation! MassDash is a visualization and data exploration platform for Data-Independent Acquisition mass spectrometry data. 

Key Features Include:

* **Chromatogram Visualization** - Easily view and analyze chromatograms for an in-depth examination of peptide precursors of interest.
* **2D and 3D Visualizations** - Visualization of ion mobility enhacanced mass spectrometry and other 2D and 3D plots.
* **On the fly parameter optimization** - Adjust peak picking parameters on the fly or experiment with novel deep learning based peak picking approaches. 
* **Algorithm testing** -  Develop and fine-tune custom algorithms by interfacing with MassDash's various data analysis algorithms and workflows.
* **Usage Flexibility** - User-friendly web based dashboard for quick visualizations, advanced python package for more complex applications 

Contribute
**********

* `Issues Tracker <https://github.com/Roestlab/massdash/issues>`_
* `Source Code <https://github.com/Roestlab/massdash/tree/main/massdash>`_

Support
*******

If you are having issues or would like to propose a new feature, please use the `issues tracker <https://github.com/Roestlab/massdash/issues>`_.

License
*******

This project is licensed under the BSD 3-Clause license.

Citation
********
If MassDash was usefull in your research please cite the following:

Sing JC, Charkow J, AlHigaylan M, Horecka I, Xu L, Röst HL. MassDash: A Web-Based Dashboard for Data-Independent Acquisition Mass Spectrometry Visualization. J Proteome Res. 2024 Jun 7;23(6):2306-2314. doi: 10.1021/acs.jproteome.4c00026. Epub 2024 Apr 29.


Please Click below for More Information:

.. toctree::
   :maxdepth: 1
   :glob:

   Installation
   GUI
   Python Interface
   API
   OSWPQ_Parser
   Plotting Gallery
   Testing