CSI:FingerID Archives - Bright Giant

Discoveries

How to Constrain the Molecular Structure Search Space with Chemical Labeling

Unlocking the chemical ‘dark matter’ in metabolomics is a persistent challenge. A new approach addresses this by integrating derivatisation reactions for chemical labeling directly into the mass spectrometry workflow. It provides crucial structural information which is fed into small molecule annotation tools like SIRIUS to significantly constrain the molecular structure search space and boost annotation accuracy, even for previously undiscovered compounds. This powerful approach offers a scalable solution to unlock the vast, uncharted chemical space of the metabolome.

Franziska Hufsky 2025-09-15 No Comments

Wooden pipe in the forest from which spring water flows

Application Notes

Detecting pharmaceuticals and their transformation products with SIRIUS

Pharmaceutical pollution poses risks to ecosystems and human health, yet traditional annotation methods often miss transformation products—drug breakdown compounds that may be even more persistent. We demonstrate how SIRIUS enhances annotation of pharmaceuticals in Luxembourgish rivers, from precursor drug screening to transformation product screening. Our approach for environmental monitoring is relevant not only for pharmaceuticals but also for pesticides and industrial chemicals, whose degradation products may have significant environmental impacts.

Franziska Hufsky 2025-04-28 No Comments

Discoveries

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 No Comments

SIRIUS Background

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 No Comments

Discoveries

a-MAIZE-ing: Sustainable Pest Control Investigated with SIRIUS

Agriculture has always been a dance with nature, requiring farmers to constantly adapt to changing conditions. One particularly promising method that has emerged over recent decades is push-pull technology, a strategy that uses nature’s own defenses to protect crops and boost yields. Using SIRIUS, researchers uncovered metabolites in push-pull maize that enhance its natural defense against pests.

Franziska Hufsky 2024-10-28 No Comments

Assorted liquor bottles in a bar. Plastic-related contaminants in liquor products were even found in glass packaging.

Discoveries

Screening extractables and leachables with SIRIUS: Plastic-related contaminants in liquor products

In a world where we’re becoming increasingly conscious of what we consume, understanding the potential presence of unexpected extractables and leachables in our food and drinks is paramount. Alcoholic beverages are of particular concern due to their increased affinity and extended storage periods. A non-targeted approach to analysis is essential for uncovering both known and unknown contaminants in our drinks. By analysing fragmentation patterns, SIRIUS predicts chemical structures of unknowns to identify unexpected contaminants and ensure safety of our food.

Franziska Hufsky 2024-09-30 No Comments

Discoveries

Thawing permafrost: Another step towards assessing the consequences

Thawing permafrost, caused by climate change, releases stored carbon into the atmosphere, accelerating global warming. The enzyme latch hypothesis suggests that low-oxygen conditions in wetlands slow down enzymatic polyphenol degradation and carbon release. But are oxygen-dependent phenol oxidases really the only enzymes that microbial communities have in their arsenal? Or should we perhaps take a closer (metatranscriptomic and metabolomic) look at the microbially catalysed carbon cycle?

Franziska Hufsky 2024-06-06 No Comments

Discoveries

Quality control using SIRIUS: nutrient profiles of Spirulina and co

Microalgae, such as Spirulina, are promising sources of sustainable nutrition with rich nutrient profiles. Ensuring consistent quality of microalgae as dietary supplements requires a quality control method reporting about their chemical composition. Mass spectrometry-based metabolomics coupled with SIRIUS helps identifying primary and secondary metabolites with potential health benefits, including free fatty acids, polar lipids, and pigments.

Franziska Hufsky 2024-03-25 No Comments

Current wastewater treatment plants often struggle to effectively remove antibiotics and their transformation products.

Discoveries

Biotransformation of antibiotics in wastewater: A fungal solution investigated with SIRIUS

Antibiotics are crucial for fighting bacterial infections, but the rise of antibiotic resistance poses a serious threat to public health. Beyond healthcare, the presence of antibiotic residues in wastewater exacerbates the problem. Conventional treatment methods often fall short in adequately removing these compounds, perpetuating resistance. Biological processes, such as biotransformation by fungi, have emerged as promising alternatives. Researchers investigated the potential of fungi to transform antibiotics, using SIRIUS and CSI:FingerID to identify degradation products.

Franziska Hufsky 2024-02-09 1 Comment