— SIRIUS Solutions for
Pharmaceuticals and drug discovery
SIRIUS helps researchers discover unknown natural products as drug candidates, map complex drug metabolites, and identify unexpected impurities and degradants during production — all from a single fragmentation mass spectrometry workflow.
Why mass spectrometry teams in pharma use SIRIUS
No spectral library is exhaustive. SIRIUS annotates molecular formulas, structures, and compound classes directly from fragmentation spectra, so novel metabolites, natural products, and degradation products can be characterized even when no matching reference spectrum exists.
Discover
Screen natural product extracts and synthetic libraries for novel bioactive small molecules.
Characterize
Map how a candidate drug is metabolized and transformed in the body, in the environment, and during formulation.
Control
Recognize unexpected impurities and degradants with reproducible annotation that feeds into a quality investigation.
Find the next drug candidate
Natural products remain one of the richest sources of new therapeutic scaffolds, but the vast majority of compounds in an extract have no entry in any spectral or structure database. SIRIUS is built for exactly this gap: it proposes molecular formulas directly from isotope and fragmentation patterns, predicts a compound’s molecular fingerprint, and uses that fingerprint to search structure databases such as PubChem — or, when nothing in any database fits, to generate candidate structures de novo.
Field example
Researchers used SIRIUS to prioritize marine microorganisms by the chemical diversity of their metabolite output, nearly doubling the number of natural products annotated and flagging under-studied strains with strong drug-discovery potential.
Molecular formula annotation without relying on a spectral library.
Molecular structure annotation by searching against built-in and custom structure databases.
De novo structure generation for compounds absent from every database.
Compound class prediction gives an immediate chemical hypothesis for completely uncharacterized hits.
Map drug metabolites, wherever they end up
Understanding what happens to a compound after it is administered — or after it is released into the environment — is central to both drug safety testing and pharmacovigilance. Metabolite and transformation product structures are rarely in any spectral library, which is precisely where SIRIUS’s library-independent annotation becomes valuable.
SIRIUS integrates BioTransformer 3.0 to automatically generate expected biotransformation products for a parent drug, and a Reaction Sketcher for defining custom transformation rules, dramatically expanding the search space beyond a fixed database.
Tranformation product prediction simplifies the annotation of drug metabolites and breakdown products.
Field example — inside the body
A study in Nature Chemistry used SIRIUS to show how gut bacteria transform 127 GPCR-targeted drugs, in some cases activating them and in others inactivating them, uncovering metabolism routes invisible to standard library search.
Field example — beyond the body
SIRIUS has been used to annotate pharmaceuticals and their transformation products in surface waters, combining precursor drug screening with degradation product screening to reveal pollutants that targeted methods miss.
Built for pharma-scale throughput
A candidate-screening campaign or a metabolite-mapping study can involve thousands of LC-MS/MS runs. SIRIUS is engineered to take a full run from hours to minutes and to fit into pipelines that already include other software.
Parameter-free LC/MS preprocessing with automatic feature detection, alignment, and adduct detection.
GUI, CLI, and API share one persistence layer, so high-throughput CLI or API runs can be inspected visually in the GUI.
Integrations with MassHunter, mzmine, and Compound Discoverer move results back into the software your lab already runs.
Computation presets save validated, reusable workflow configurations for recurring study types.
Field example — screening at scale
A study with FSU Jena, Leiden University, and Oncode Institute introduced barcode-free Self-Encoded Libraries, screening over half a million small molecules in one experiment and using SIRIUS-COMET to reconstruct ligand structures from their own mass signature instead of a DNA tag — unlocking targets that tag-based screening couldn’t reach.
Confidence you can put in a report
Recognizing an unexpected impurity or degradant means dealing with a compound that has no entry in any spectral library — and then judging how much to trust the identification before it goes into a quality investigation. SIRIUS pairs its formula and structure annotation with explicit, exportable confidence measures at every step.
Confidence score rates how likely a structure hit is to be exactly correct, or to be highly similar to the true structure.
Substructure validation links specific fragment or neutral-loss peaks in a spectrum to substructures of a candidate, so an annotation can be checked peak by peak
Spectral library and analog matching cross-checks results against in-house reference libraries where they exist
See what SIRIUS finds in your data
Millions of queries are processed every year in SIRIUS to characterize the compounds that spectral libraries can’t. Bring your fragmentation data and see what surfaces.
Related solutions
Environmental and Water Analysis
Pharmaceutical pollutants and transformation products
Metabolism and Biotransformations
Endogenous and microbial metabolite mapping
Clinical Research and Diagnostics
Biomarker discovery in patient cohorts
Identifying novel psychoactive substances
Explore more on the blog
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For Research Use Only. Not for use in diagnostic procedures.