StructureMASST enables pan-repository MS/MS searches using a chemical name or structure.

The exponential growth of untargeted metabolomics data, now reaching billions of mass spectra in public repositories, benefits from reannotation strategies for data reuse. While tandem mass spectromet...

Mass spectrometry data mining tools enabled the creation of an MS/MS spectral library containing hundreds of N-acyl lipids, including conjugates with short-chain fatty acids. This resource enabled the...

Using mass spectrometry-based tools to mine public untargeted MS/MS data revealed the vastly underappreciated diversity of bile acids hidden in plain sight and led to the discovery of previously unkno...

The etiology of Alzheimer’s Disease (AD) remains largely unclear but is likely driven by gene-environment interactions. Here, we present a multi-organ untargeted metabolomics dataset (2,271 samples) g...

In this reverse metabolomics protocol, a tandem mass spectrometry spectrum is used as a search term to probe public metabolomic data. Analysis of the metadata connected with these search results enabl...

Untargeted metabolomics is frequently performed on human fecal samples in conjunction with sequencing to unravel the gut microbiome functionality. As sample collection efforts are rapidly expanding, with individuals often collecting specimens at home, metabolomics experiments should adapt to accommodate the safety and needs of bulk off-site collections and improve high throughput. Here, we show that a 95% ethanol, safe to be shipped and handled, extraction part of the Matrix Method pipeline recovers comparable amounts of metabolites as a validated 50% methanol extraction, preserving metabolic profile differences between investigated subjects. Additionally, we show that the fecal metabolome remains relatively stable when stored in 95% ethanol for up to 1 week at room temperature. Finally, we suggest a metabolomics data analysis workflow based on robust centered log ratio transformation, which removes the variance introduced by possible different sample weights and concentrations, allowing for reliable and integration-ready untargeted metabolomics experiments in gut microbiome research.

Nature Metabolism - Discovery of metabolites prevails amid in-source fragmentation

Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based...

Full-scan mass spectrometry (MS) data from both liquid chromatography (LC) and MS imaging capture multiple ion forms, including their in-source fragments. Here we leverage such fragments to structural...

N -acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N -acyl lipids with untargeted mass spectrometry-based...