LC-MS/MS Spectrum Prediction

Goal

Predict the LC-MS/MS (tandem mass) spectrum of a molecule given its SMILES string using ICEBERG — a two-stage GNN that first generates a fragmentation DAG (fragment ions) and then predicts their intensities. Output is a predicted spectrum (m/z, intensity) with optional fragment SMILES assignments per peak.

When to Use This Skill

• A SMILES string is known and a predicted LC-MS/MS spectrum (m/z vs intensity) is needed.
• Fragment ion assignments (SMILES per peak) are required.
• No reference spectrum exists, or comparison to a predicted spectrum is desired.
• Companion skill chem-spectrum-matcher can compare predicted vs experimental spectra.

When NOT to Use This Skill

• Experimental spectrum already available — use it directly; no prediction needed.
• Only compound name known — first resolve to SMILES via drug-db-pubchem, then call this skill.
• GC-MS or other MS types — ICEBERG is trained on LC-MS/MS only; flag a warning before proceeding.
• Organometallics or MW > 1000 — predictions may be unreliable or fail due to unsupported element types.