chemical classification Archives

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.

Franziska Hufsky 2026-09-29 No Comments

Close-up of deep purple monkshood flowers (Aconitum) in bloom with green meadow softly blurred in the background

Discoveries

Solving the Wolf’s Bane Puzzle: Breaking the Synthesis Bottleneck for Diterpenoid Alkaloid Therapeutics

Diterpenoid alkaloids represent an exceptionally complex class of plant metabolites, highly valued for their therapeutic properties. But their extreme structural complexity makes chemical synthesis practically unfeasible, while their trace abundance in wild plants creates a massive bottleneck for pharmaceutical scale-up. Bio-manufacturing in heterologous hosts offers a viable alternative. But how do these plants assemble the highly complex, medicinal alkaloids and what is the exact origin of their nitrogen building blocks?

Franziska Hufsky 2026-07-07 1 Comment

A passageway in a cave whose walls are coloured red by the iron-rich rock

Discoveries

Exploring the Chemical Dark Matter of the Amazon’s Iron Caves with SIRIUS

Deep within the aphotic zones of the Amazon’s ferruginous caves, a hidden world of microbial “dark matter” holds immense potential as a source for pharmacological innovation. A pioneering metabolomic survey of these extreme environments isolates rare bacterial genera that thrive in these iron-rich landscapes. They use SIRIUS to identify and classify chemical features, including potent cyclopeptides demonstrating growth inhibition against cancer cell lines.

Franziska Hufsky 2026-04-23 1 Comment

An offshore platform with lots of cranes. The sea and mountains can be seen in the background

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.

Franziska Hufsky 2026-03-19 1 Comment

A mother lovingly holding her child on her lap

Discoveries

Environmental and Maternal Drivers of the Infant Gut Metabolome Revealed Using SIRIUS

The maturation of the gut microbiome during the first six months of life is a foundational process, playing a key role in metabolic programming and training of the immune system, but these patterns remain critically underexplored in populations from low- and middle-income countries. To address this gap, an observational, longitudinal study profiled the developing gut microbiome and metabolome in Bangladesh using a multi-omics approach. Systematic classification and metabolite annotation was achieved using SIRIUS. The overall aim was to understand how maternal and environmental factors—specifically delivery mode, maternal milk composition, and household water treatment—shape this foundational postnatal development.

Franziska Hufsky 2026-02-24 1 Comment

Discoveries

SIRIUS in the Jena Experiment: It’s a Battle for Resources, Not a Break from Pests

In a biodiverse ecosystem, it’s often assumed that plants have safety in numbers—that a mix of species will confuse pests and dilute disease pressure, allowing individual plants to save energy on defences and focus on growth. But is this ecological truism always the case? A recent study from the long-running Jena Experiment uses untargeted metabolomics and SIRIUS for feature annotation and compound class prediction. They found that for many plants in a diverse community it is less about relaxing their defences and more about adapting to intense competition for light and nutrients.

Franziska Hufsky 2025-11-18 1 Comment

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.

Franziska Hufsky 2025-11-11 1 Comment

Collaborations

Unlocking a Greater Perspective: Mapping the Chemical Space of Biomes Using SIRIUS

Untargeted mass spectrometry is a powerful tool for analyzing the immense chemical complexity of natural environments. However, interpreting such large datasets remains a significant challenge. To overcome this, researchers have developed an innovative approach using SIRIUS that prioritizes chemical profiling over exhaustive identification. This method allows for more effective comparisons of (micro-)biomes, providing deeper insights into biochemical diversity across different environments.

Franziska Hufsky 2025-02-13 1 Comment

Collaborations

Why Training Data Matters: Exploring Coverage Bias in Small Molecule Machine Learning

Machine learning is transforming analytical chemistry by enabling predictions of small molecule properties, crucial for drug development and other applications. However, ensuring reliable results requires careful selection of training data to avoid biases that can mislead models. Here, we explain why it was important to prepare high-quality training datasets for the machine learning methods in SIRIUS, especially given that many widely used datasets fail to evenly represent the diversity of biomolecular structures.

Franziska Hufsky 2025-01-20 1 Comment

Chemical Classification