Untargeted metabolomics strategies—challenges and emerging directions

AC Schrimpe-Rutledge, SG Codreanu… - Journal of the …, 2016 - ACS Publications
Metabolites are building blocks of cellular function. These species are involved in enzyme-
catalyzed chemical reactions and are essential for cellular function. Upstream biological …

Software tools and approaches for compound identification of LC-MS/MS data in metabolomics

I Blaženović, T Kind, J Ji, O Fiehn - Metabolites, 2018 - mdpi.com
The annotation of small molecules remains a major challenge in untargeted mass
spectrometry-based metabolomics. We here critically discuss structured elucidation …

Feature-based molecular networking in the GNPS analysis environment

LF Nothias, D Petras, R Schmid, K Dührkop, J Rainer… - Nature …, 2020 - nature.com
Molecular networking has become a key method to visualize and annotate the chemical
space in non-targeted mass spectrometry data. We present feature-based molecular …

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

H Tsugawa, T Cajka, T Kind, Y Ma, B Higgins, K Ikeda… - Nature …, 2015 - nature.com
Data-independent acquisition (DIA) in liquid chromatography (LC) coupled to tandem mass
spectrometry (MS/MS) provides comprehensive untargeted acquisition of molecular data …

A lipidome atlas in MS-DIAL 4

H Tsugawa, K Ikeda, M Takahashi, A Satoh… - Nature …, 2020 - nature.com
Abstract We present Mass Spectrometry-Data Independent Analysis software version 4 (MS-
DIAL 4), a comprehensive lipidome atlas with retention time, collision cross-section and …

CFM-ID 4.0: more accurate ESI-MS/MS spectral prediction and compound identification

F Wang, J Liigand, S Tian, D Arndt, R Greiner… - Analytical …, 2021 - ACS Publications
In the field of metabolomics, mass spectrometry (MS) is the method most commonly used for
identifying and annotating metabolites. As this typically involves matching a given MS …

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 …

Searching molecular structure databases with tandem mass spectra using CSI: FingerID

K Dührkop, H Shen, M Meusel… - Proceedings of the …, 2015 - National Acad Sciences
Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics
experiments usually rely on tandem MS to identify the thousands of compounds in a …

MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation

Z Pang, Y Lu, G Zhou, F Hui, L Xu, C Viau… - Nucleic Acids …, 2024 - academic.oup.com
We introduce MetaboAnalyst version 6.0 as a unified platform for processing, analyzing, and
interpreting data from targeted as well as untargeted metabolomics studies using liquid …

Structural basis of tethered agonism of the adhesion GPCRs ADGRD1 and ADGRF1

X Qu, N Qiu, M Wang, B Zhang, J Du, Z Zhong, W Xu… - Nature, 2022 - nature.com
Adhesion G protein-coupled receptors (aGPCRs) are essential for a variety of physiological
processes such as immune responses, organ development, cellular communication …