Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools
NF de Jonge, K Mildau, D Meijer, JJR Louwen… - Metabolomics, 2022 - Springer
Background Untargeted metabolomics approaches based on mass spectrometry obtain
comprehensive profiles of complex biological samples. However, on average only 10% of …
comprehensive profiles of complex biological samples. However, on average only 10% of …
Regulatory T cells shield muscle mitochondria from interferon-γ–mediated damage to promote the beneficial effects of exercise
Exercise enhances physical performance and reduces the risk of many disorders such as
cardiovascular disease, type 2 diabetes, dementia, and cancer. Exercise characteristically …
cardiovascular disease, type 2 diabetes, dementia, and cancer. Exercise characteristically …
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
F Huber, L Ridder, S Verhoeven… - PLoS computational …, 2021 - journals.plos.org
Spectral similarity is used as a proxy for structural similarity in many tandem mass
spectrometry (MS/MS) based metabolomics analyses such as library matching and …
spectrometry (MS/MS) based metabolomics analyses such as library matching and …
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra
Mass spectrometry data is one of the key sources of information in many workflows in
medicine and across the life sciences. Mass fragmentation spectra are generally considered …
medicine and across the life sciences. Mass fragmentation spectra are generally considered …
Navigating common pitfalls in metabolite identification and metabolomics bioinformatics
EM Novoa-del-Toro, M Witting - Metabolomics, 2024 - Springer
Background Metabolomics, the systematic analysis of small molecules in a given biological
system, emerged as a powerful tool for different research questions. Newer, better, and …
system, emerged as a powerful tool for different research questions. Newer, better, and …
Flash entropy search to query all mass spectral libraries in real time
Public repositories of metabolomics mass spectra encompass more than 1 billion entries.
With open search, dot product or entropy similarity, comparisons of a single tandem mass …
With open search, dot product or entropy similarity, comparisons of a single tandem mass …
Annotating metabolite mass spectra with domain-inspired chemical formula transformers
Metabolomics studies have identified small molecules that mediate cell signaling,
competition and disease pathology, in part due to large-scale community efforts to measure …
competition and disease pathology, in part due to large-scale community efforts to measure …
Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights N-acylnornicotine innovations
Specialized metabolite (SM) diversification is a core process to plants' adaptation to diverse
ecological niches. Here, we implemented a computational mass spectrometry–based …
ecological niches. Here, we implemented a computational mass spectrometry–based …
MS2Query: reliable and scalable MS2 mass spectra-based analogue search
NF de Jonge, JJR Louwen, E Chekmeneva… - Nature …, 2023 - nature.com
Metabolomics-driven discoveries of biological samples remain hampered by the grand
challenge of metabolite annotation and identification. Only few metabolites have an …
challenge of metabolite annotation and identification. Only few metabolites have an …
Comparison of cosine, modified cosine, and neutral loss based spectrum alignment for discovery of structurally related molecules
Spectrum alignment of tandem mass spectrometry (MS/MS) data using the modified cosine
similarity and subsequent visualization as molecular networks have been demonstrated to …
similarity and subsequent visualization as molecular networks have been demonstrated to …