API Reference¶

Welcome to the MS2LDA API reference documentation. This section provides detailed information about all the modules, classes, and functions available in MS2LDA.

Overview¶

MS2LDA is organized into several main components:

Core Modules: The fundamental components for running MS2LDA analysis
Add-On Modules: Additional functionality for enhanced analysis
Visualization: Tools for visualizing results

Core Modules¶

MS2LDA Run ¶

The main entry point for running MS2LDA analysis. Contains functions for executing the complete workflow.

Modeling ¶

Core LDA modeling functionality including model training and inference.

Mass2Motif ¶

Classes and functions for handling Mass2Motif objects and operations.

Preprocessing ¶

Data preprocessing utilities for preparing mass spectrometry data for analysis.

Add-On Modules¶

Fingerprints ¶

Molecular fingerprint calculation and substructure retrieval functionality.

MassQL ¶

MassQL query language support for searching and filtering mass spectrometry data.

NTS ¶

Non-target screening tools for environmental analysis.

Spec2Vec ¶

Spec2Vec integration for spectral similarity calculations and annotation.

Visualization¶

Visualization Tools ¶

Comprehensive visualization utilities for exploring MS2LDA results.

Quick Start¶

To use MS2LDA programmatically:

from MS2LDA import run_ms2lda
from MS2LDA.Preprocessing import load_and_clean

# Load and preprocess data
spectra = load_and_clean.load_mgf("your_data.mgf")

# Run MS2LDA
results = run_ms2lda(spectra, n_motifs=200)

For detailed usage examples, see the Examples section.