High resolution mass spectrometry based techniques at the crossroads of metabolic pathways

C Junot, F Fenaille, B Colsch… - Mass spectrometry …, 2014 - Wiley Online Library
The metabolome is the set of small molecular mass compounds found in biological media,
and metabolomics, which refers to as the analysis of metabolome in a given biological …

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics

A Vaniya, O Fiehn - TrAC Trends in Analytical Chemistry, 2015 - Elsevier
Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving
interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is …

Fragmentation trees reloaded

S Böcker, K Dührkop - Journal of cheminformatics, 2016 - Springer
Background Untargeted metabolomics commonly uses liquid chromatography mass
spectrometry to measure abundances of metabolites; subsequent tandem mass …

Computational mass spectrometry for small molecules

K Scheubert, F Hufsky, S Böcker - Journal of cheminformatics, 2013 - Springer
The identification of small molecules from mass spectrometry (MS) data remains a major
challenge in the interpretation of MS data. This review covers the computational aspects of …

Substructure‐based annotation of high‐resolution multistage MSn spectral trees

L Ridder, JJJ van der Hooft… - Rapid …, 2012 - Wiley Online Library
RATIONALE High‐resolution multistage MSn data contains detailed information that can be
used for structural elucidation of compounds observed in metabolomics studies. However …

Computational mass spectrometry for small-molecule fragmentation

F Hufsky, K Scheubert, S Böcker - TrAC Trends in Analytical Chemistry, 2014 - Elsevier
The identification of small molecules from mass spectrometry (MS) data remains a major
challenge in the interpretation of MS data. Computational aspects of identifying small …

Automatic Chemical Structure Annotation of an LC–MSn Based Metabolic Profile from Green Tea

L Ridder, JJJ van der Hooft, S Verhoeven… - Analytical …, 2013 - ACS Publications
Liquid chromatography coupled with multistage accurate mass spectrometry (LC–MS n) can
generate comprehensive spectral information of metabolites in crude extracts. To support …

General principles of identification by mass spectrometry

BL Milman - TrAC Trends in Analytical Chemistry, 2015 - Elsevier
The review is devoted to chemical identification using mass spectrometry as the most
powerful technique of qualitative analysis. The review begins with consideration of basic …

Identifying the unknowns by aligning fragmentation trees

F Rasche, K Scheubert, F Hufsky, T Zichner… - Analytical …, 2012 - ACS Publications
Mass spectrometry allows sensitive, automated, and high-throughput analysis of small
molecules. In principle, tandem mass spectrometry allows us to identify “unknown” small …

A map of mass spectrometry-based in silico fragmentation prediction and compound identification in metabolomics

CA Krettler, GG Thallinger - Briefings in Bioinformatics, 2021 - academic.oup.com
Metabolomics, the comprehensive study of the metabolome, and lipidomics—the large-scale
study of pathways and networks of cellular lipids—are major driving forces in enabling …