MS Fragmenter™

MS Fragmenter is a mass spectrometry software tool that predicts MS fragment ions directly from a chemical structure. It helps chemists interpret mass spectra, assign fragment ions, and confidently characterize compounds without prior experimental data. It is widely used in impurity profiling, metabolite identification, and unknown compound characterization across pharmaceutical and chemical research.

MS Fragmenter is designed for analytical chemists, mass spectrometrists, and scientists in pharmaceutical, biotech, chemical, and environmental industries. It supports small molecules including APIs, metabolites, impurities, degradants, and reaction mixtures, helping teams accelerate structure elucidation and improve confidence in analytical decision-making.

Identify unknown compounds by matching experimental MS/MS fragment ions to predicted fragmentation patterns from candidate structures. MS Fragmenter supports data acquisition, candidate structure generation, in silico fragmentation prediction, and spectral comparison—helping scientists quickly prioritize, confirm, or eliminate structures with higher confidence and faster decision-making.

Yes, MS Fragmenter compares predicted fragmentation patterns with experimental mass spectra to confirm structural assignments. It uses advanced algorithms to match theoretical fragments against observed peaks, enabling confident structure elucidation, impurity identification, and metabolite characterization with visual comparison tools. 

Fragmentation prediction can support a wide range of mass spectrometry workflows, including LC/MS, LC/MS/MS, GC/MS, GC/MS/MS, and high-resolution mass spectrometry (HRMS). It is particularly valuable for analyzing small molecules, pharmaceutical impurities, degradants, metabolites, reaction products, and unknown compounds where structural confirmation is required.

Spectral libraries are valuable when reference spectra exist, but many compounds, including novel impurities, degradants, metabolites, and proprietary molecules may not be represented in available databases. Fragmentation prediction provides structure-based evidence that can help identify compounds even when no library match is available.

Unlike basic rule-based calculators that generate theoretical fragments, MS Fragmenter helps scientists connect predicted fragments to experimental spectra and evaluate structural hypotheses within a broader analytical workflow. This provides greater context for spectral interpretation and supports more informed decision-making.

MS Fragmenter is part of the Spectrus Platform, which is designed to support data integration across analytical workflows. This helps laboratories working with multiple instrument vendors standardize data interpretation, improve collaboration, and maintain consistency across projects.
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