Delivering confidence for small molecule identification

Importance of the Topic

Accurate identification of small molecules in complex samples is critical for applications ranging from metabolomics to clinical toxicology and environmental analysis. High-confidence assignments reduce the need for reanalysis, accelerate workflows, and support regulatory compliance. Mass spectral libraries combined with robust software tools provide a reliable foundation for routine and research LC-MS based investigations.

Objectives and Study Overview

This white paper introduces an integrated solution for small molecule identification using a high-quality online spectral library (mzCloud) and accompanying desktop software (mzVault) supported by the Thermo Orbitrap platform. The goal is to demonstrate how extensive curation, multi-level MSn data, and advanced search algorithms can address the challenges of both targeted screening and unknown discovery.

Used Methodology and Instrumentation

The core spectral data are acquired on high-resolution accurate-mass Orbitrap mass spectrometers using both collision–induced dissociation (CID) and higher-energy collisional dissociation (HCD). Fragmentation spectra spanning multiple energy levels and MS stages (up to MS4 or beyond) are collected for each adduct form. Raw spectra undergo noise filtering, recalibration, averaging, and expert manual annotation of fragment structures and formulas.

Main Results and Discussion

mzCloud currently contains over 8 000 compound entries and nearly 2.8 million curated spectra covering positive and negative ion modes. Each compound record includes annotated spectral trees, instrument metadata, collision energies, and structural identifiers (InChI, InChIKey). The multi-energy approach and manual curation yield high match confidence and support energy breakdown curve visualization for rapid method optimization. Offline libraries created with mzVault and in-house curation tools expand the repository for proprietary or custom analytes. Integration with Compound Discoverer enables seamless unknown searches and similarity ranking via the mzLogic algorithm, while TraceFinder leverages mzVault libraries for targeted screening.

Benefits and Practical Applications

• Enhanced identification confidence through curated high-resolution MSn spectra
• Wide chemical coverage including metabolites, pharmaceuticals, toxins, and industrial chemicals
• Custom library creation for proprietary compounds and repeat unknowns
• Streamlined workflow from data acquisition to actionable results in both research and regulated environments

Future Trends and Applications

Continued expansion of spectral libraries will incorporate novel compounds and additional fragmentation pathways. Advances in machine learning and in silico prediction will further augment curation efficiency and similarity scoring. Cloud-based sharing of curated libraries can foster collaborative annotation and accelerate discovery across laboratories.

Conclusion

The combination of the extensively curated mzCloud online library and the flexible mzVault software delivers a comprehensive platform for small molecule identification. High-quality Orbitrap MSn data, multi-energy fragmentation, and integrated search workflows offer laboratories the tools needed to achieve rapid, reliable results in both targeted and untargeted applications.

Reference

No additional literature references were provided in the source document.