Skip to content

MS2LDAViz — Interactive Web Interface 🌐

MS2LDAViz lets you run analyses and explore your results in your browser, with live controls and rich visualizations.

1. Launching the App

The MS2LDA repository includes convenient scripts that allow the easy access to the Viz App. If you have not cloned the repository and created a conda enviroment, please go to Getting Started, afterwards you will find inside the MS2LDA folder the following scripts:

  • run_ms2ldaviz.sh (Linux/macOS)
  • run_ms2ldaviz.bat (Windows)

In order to use the scripts please type:

# For Linux/macOS
./run_ms2ldaviz.sh

# For Windows 
./run_ms2ldaviz.bat

Aftewards you will be redirected to the following website (http://127.0.0.1:8000/….)

Website page

There you could access different tabs, explained below:

  • Run Analysis: Upload your MS/MS spectra (positive/negative ion mode), set core parameters, and start a new run. Note: Before running MS2LDA you must download the Spec2Vec model, embeddings, and library DB (See the Zenodo repository).

Zenodo

  • Load Results: Open a previous MS2LDA run (compressed JSON format) or load a demo dataset. After the run finishes, the other tabs will automatically be updated.

Load results

  • Motif Rankings: Browse all Mass2Motifs ranked based on different tresholds, or search for specific motifs using MassQL queries. You can click a motif to view its details on the next tab.

Motif rankings

  • Motif Details: Inspect selected motifs in depth: suggested structures/annotations from MAG, fragment and neutral-loss composition in optimized pseudo-spectra based on probability filters, and the spectra that load on it.

Motif details

  • Spectra Search: Find individual spectra by parent mass or fragment/loss values, and check their spectra and associated motifs.

Spectra search

  • View Network: Explore an interactive network of optimized motifs, where each M2M is displayed as a node connected to its fragments ands losses.

Motif network

  • Motif Search: Perform motif-motif searches against reference motifs in MotifDB. This updates the Motif annotations in previous tabs.

Motif search

Ready to jump to the Command-line? Then see 💻 otherwise please refer to our "Examples and Tutorials" 📚

Command-line Guide Examples & Tutorials