Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

S Alseekh, A Aharoni, Y Brotman, K Contrepois… - Nature …, 2021 - nature.com
Mass spectrometry-based metabolomics approaches can enable detection and
quantification of many thousands of metabolite features simultaneously. However …

Small molecule metabolites: discovery of biomarkers and therapeutic targets

S Qiu, Y Cai, H Yao, C Lin, Y **e, S Tang… - Signal Transduction and …, 2023 - nature.com
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite
accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite …

Integrative analysis of multimodal mass spectrometry data in MZmine 3

R Schmid, S Heuckeroth, A Korf, A Smirnov… - Nature …, 2023 - nature.com
Innovation in mass spectrometry (MS) and the rapidly increasing throughput and sensitivity
of MS instrumentation require adaptations and innovations in data processing tools. Here …

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra

K Dührkop, LF Nothias, M Fleischauer, R Reher… - Nature …, 2021 - nature.com
Metabolomics using nontargeted tandem mass spectrometry can detect thousands of
molecules in a biological sample. However, structural molecule annotation is limited to …

High-confidence structural annotation of metabolites absent from spectral libraries

MA Hoffmann, LF Nothias, M Ludwig… - Nature …, 2022 - nature.com
Untargeted metabolomics experiments rely on spectral libraries for structure annotation, but,
typically, only a small fraction of spectra can be matched. Previous in silico methods search …

Comprehensive investigation of pathway enrichment methods for functional interpretation of LC–MS global metabolomics data

Y Lu, Z Pang, J **a - Briefings in Bioinformatics, 2023 - academic.oup.com
Background: Global or untargeted metabolomics is widely used to comprehensively
investigate metabolic profiles under various pathophysiological conditions such as …

Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity

JP Shaffer, LF Nothias, LR Thompson, JG Sanders… - Nature …, 2022 - nature.com
Despite advances in sequencing, lack of standardization makes comparisons across studies
challenging and hampers insights into the structure and function of microbial communities …

Reverse metabolomics for the discovery of chemical structures from humans

EC Gentry, SL Collins, M Panitchpakdi, P Belda-Ferre… - Nature, 2024 - nature.com
Determining the structure and phenotypic context of molecules detected in untargeted
metabolomics experiments remains challenging. Here we present reverse metabolomics as …

Enigmatic persistence of dissolved organic matter in the ocean

T Dittmar, ST Lennartz, H Buck-Wiese… - Nature Reviews Earth & …, 2021 - nature.com
Marine dissolved organic matter (DOM) contains more carbon than the combined stocks of
Earth's biota. Organisms in the ocean continuously release a myriad of molecules that …

Challenges and opportunities in sharing microbiome data and analyses

C Huttenhower, RD Finn, AC McHardy - Nature Microbiology, 2023 - nature.com
Microbiome data, metadata and analytical workflows have become 'big'in terms of volume
and complexity. Although the infrastructure and technologies to share data have been …