V2.0

MS2LDA v2.0.0 🚀

Major release with 14x performance improvement and automated annotation!

Key Highlights

🏎️ Performance

• 14x faster than v1 - analyze datasets in minutes instead of hours
• Modern Python implementation with optimized algorithms

🤖 Automated Annotation (MAG)

• Spec2Vec integration automatically suggests motif annotations
• No more manual annotation - AI-powered structural interpretation

🎨 Enhanced Visualization

• Interactive web interface (MS2LDAViz)
• Real-time exploration with Dash/Plotly
• Network visualization and publication-ready exports

🔍 MassQL Integration

• Query motifs using powerful MassQL syntax
• Find motifs containing specific fragments: WHERE MS2PROD=178.03
• Filter by metadata: METAFILTER:motif_id=motif_123
• Combine multiple criteria for complex searches
• Export results for downstream analysis

📚 MotifDB

• Comprehensive database of known MS/MS motifs
• Curated structural patterns from various compound classes
• Searchable by fragment patterns and annotations
• Continuously updated with community contributions

Citation

Torres Ortega et al. (2025). Large-scale discovery and annotation of hidden substructure patterns in mass spectrometry profiles. bioRxiv. doi: 10.1101/2025.06.19.659491.

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Install now: pip install ms2lda

New Contributors

• @rtlortega made their first contribution in #2
• @j-a-dietrich made their first contribution in #3
• @joewandy made their first contribution in #7