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MS2LDA User Guide Overview

MS2LDA’s functionality is organized into modular steps, each performing a discrete task on your MS/MS data. Below is just a high‑level overview of the process.

Modules at a Glance:

• Preprocessing → filter & clean your spectra (positive/negative ion mode)

• Modeling → infer Mass2Motifs via LDA

• Annotation → assign substructure meaning (currently MAG is trained on positive ionization mode data)

• Visualization → explore and export results

All modules are explained in detail in the Modules Reference tab.

Try the MS2LDAViz 2.0 website in your browser. Here you can load previously generated results file or explore one of the demo datasets:

Website page

Running MS2LDA 🚀

For further details on how run MS2LDA 2.0 using the Viz App or the Command-Line, click below:

  1. MS2LDAViz App

  2. Command‑Line Interface