Tutorials¶
This section contains step-by-step tutorials for using MS2LDA.
Basic MS2LDA Analysis¶
A complete walkthrough of running MS2LDA on your mass spectrometry data.
Loading Data¶
from MS2LDA.Preprocessing import load_and_clean
# Load MGF file
spectra = load_and_clean.load_mgf("your_data.mgf")
Running MS2LDA¶
from MS2LDA import run
# Run with default parameters
results = run.run_ms2lda(spectra, n_motifs=200)
Visualizing Results¶
from MS2LDA.Visualisation import MS2LDA_visualisation
# Create visualization
MS2LDA_visualisation.plot_motifs(results)
Advanced Topics¶
- Working with MotifDB
- Custom preprocessing pipelines
- Integration with other tools
For more examples, see the notebooks directory in the repository.