Molecular Structure Annotation

SIRIUS uses the molecular fingerprint to efficiently search massive molecular structure databases to identify the most likely structure candidate for your unknown compound. SIRIUS ships with a wide range of built-in databases. By default, SIRIUS searches in a biomolecule structure database. It can also search in the (extremely large) PubChem database. Additionally, users can enhance the search capabilities by adding custom databases with their own structures.

This archive showcases discoveries and major breakthroughs made by research groups worldwide using the SIRIUS’ molecular structure annotation feature.

A close-up shot of an infant lying on a table in a health clinic setting. The baby's shirt is lifted to reveal their bare belly, where a mother's hand gently rests. Medical posters and clinic paperwork are visible in the background.
Discoveries

How SIRIUS Mapped the Chemical Shield Against “Superbugs” in the Infant Gut

Antimicrobial resistance in early life represents a critical global health challenge, particularly in low- and middle-income countries. Researchers investigated whether early-life oral probiotic supplementation can metabolically reprogram the infant gut microbiome to exclude antibiotic-resistant superbugs. Using SIRIUS-powered untargeted metabolomics, the team elucidated the resulting metabolic reprogramming. They found that high levels of beneficial Bifidobacterium drives a protective environment flooding the gut with organic acids and creating a protective chemical shield against drug-resistant Enterobacterales.

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Collaborations

How to… use the SIRIUS API for Untargeted Differential LC-MS/MS Analysis

Pipelines incorporating fragmented tools and manual file transfers severely limit research reproducibility. The release of SIRIUS 6 introduces a RESTful API that allows researchers to access the powerful SIRIUS annotation tools directly within a unified Python environment. In this tutorial, we show how the PySirius library automates the entire end-to-end workflow, from raw data to structure annotation.

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Discoveries

SIRIUS-ly Toxic: Mapping Unknown Urinary Biomarkers Derived from Deep-Fried Foods

Every day, our bodies encounter millions of foreign chemical compounds. Among the most dangerous are reactive electrophilic species—unstable molecules that can bind to DNA and proteins, potentially leading to chronic diseases. Fortunately, our bodies fight back using glutathione conjugation, excreting these toxins as urinary mercapturic acid conjugates (MACs). But until now, checking urine to see exactly what toxins we’ve been exposed to was incredibly difficult because standard tracking methods miss highly unstable chemical structures. Researchers developed an analytical strategy that dramatically expands our ability to profile the urinary “adductome”. By pairing high-resolution mass spectrometry with customized database construction and automated computational annotation using SIRIUS, this workflow uncovers hundreds of previously untraceable biomarkers.

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Assorted colorful prescription pills, capsules, and tablets spilled out of an open glass medicine bottle
Discoveries

SIRIUS 🤝 BioTransformer: A Dream Team for Unraveling Drug Metabolism

Understanding the metabolic fate of pharmaceutical drugs is a critical component of modern drug discovery and safety testing. Tracking these metabolic changes is notoriously difficult. Identifying the precise structures of drug metabolites within complex mixtures remains a massive analytical bottleneck. To overcome this hurdle, we have integrated BioTransformer in SIRIUS. Researchers have benchmarked this approach using six diverse model drugs and found that it not only bypasses the need for exhaustive manual identification but actively expands our structural coverage of the metabolome.

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Discoveries

Cultural Heritage Preservation: SIRIUS for Identifying Yellow Dye Markers

Identifying the botanical origins of yellow dyes in ancient textiles is a notorious challenge due to the chemical overlap of common pigments across different plant species. This study introduces a robust metabolomics workflow designed to move beyond ubiquitous molecules like quercetin to find species-specific “Gold” chemical markers using SIRIUS.

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Close-up of a fern frond
Discoveries

Discovering a Novel Phenolic Compound in Fern With SIRIUS

The specialized metabolism of ferns remains a largely untapped frontier in the search for natural medicinal compounds. Using SIRIUS molecular structure annotation, researchers successfully identified a previously unknown lignan named blechnic acid B. This novel compound, found in Neoblechnum brasiliense, highlights the chemical diversity hidden within under-investigated plant lineages.

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Discoveries

Revealing the Hidden Burden of Offshore Discharges with SIRIUS

Offshore produced water discharges introduce over 240 billion liters of complex chemical mixtures into the marine environment annually. In a case study using produced water from North Sea offshore oil platforms, researchers demonstrated that traditional monitoring significantly underestimates the persistence of discharged chemicals. They introduce a novel analytical framework using advanced non-target analysis and computational workflows, including SIRIUS to highlight a significant “hidden burden” of persistent pollutants.

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Discoveries

SIRIUS in Space: The ISS metabolome

As we prepare for longer human missions beyond Earth, understanding the invisible ecosystems of space habitats has become critical for astronaut health. The International Space Station (ISS) is not just a home and laboratory—it is also a closed microbial and chemical environment unlike anything on Earth. This study mapped the ISS microbiome and metabolome in unprecedented detail, uncovering its vast chemical “dark matter” using SIRIUS.

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Collaborations

Going Barcode-Free: Screening Massive Small Molecule Libraries for Early Drug Discovery

Our recent study co-authored by researchers at Bright Giant, FSU Jena, Leiden University and Oncode Institute introduces a major leap forward in affinity selection screening for early drug discovery: Self-Encoded Libraries. Our approach uses advanced mass spectrometry to screen hundreds of thousands of small molecules in a single experiment, bypassing the significant limitations of traditional high-throughput screening as well as affinity selection with barcoded libraries. It allows drug discovery teams to identify high-affinity drug candidates faster, more affordably, and against targets previously inaccessible to common screening methods.

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