Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree
Anupriya Tripathi
Yoshiki Vázquez-Baeza
Julia M. Gauglitz
Mingxun Wang
Kai Dührkop
Mélissa Nothias-Esposito
Deepa D. Acharya
Madeleine Ernst
Justin J.J. van der Hooft
Qiyun Zhu
Daniel McDonald
Antonio Gonzalez
Jo Handelsman
Markus Fleischauer
Marcus Ludwig
Sebastian Böcker
Louis-Félix Nothias
Rob Knight
Pieter C. Dorrestein
[], 2020-5-5
Julia Gauglitz
Gauglitz Julia
/ Julia M. Vraspir
ORCID: 0000-0003-3146-2489
Amphiphilic siderophore production by oil-associating microbes
10.1039/c4mt00047a
Microbial Tailoring of Acyl Peptidic Siderophores
10.1021/bi500266x
A suite of citrate-derived siderophores from a marine Vibrio species isolated following the Deepwater Horizon oil spill
10.1016/j.jinorgbio.2011.10.013
Optical Signatures of Dissolved Organic Matter Transformation in the Global Ocean
10.3389/fmars.2015.00118
Amino acid variability in the peptide composition of a suite of amphiphilic peptide siderophores from an open ocean Vibrio species
10.1007/s00775-013-0995-3
Identification of new members within suites of amphiphilic marine siderophores
10.1007/s10534-010-9378-1
Chemistry of Marine Ligands and Siderophores
10.1146/annurev.marine.010908.163712
Both Incubation Temperature and Posthatching Temperature Affect Swimming Performance and Morphology of Wood Frog Tadpoles ( Rana sylvatica )
10.1086/498182
Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages
10.1101/347716
Untargeted Mass Spectrometry-Based Metabolomics Approach Unveils Molecular Changes in Raw and Processed Foods and Beverages
10.1016/j.foodchem.2019.125290
Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs
10.1101/790063
Native Electrospray-based Metabolomics Enables the Detection of Metal-binding Compounds
10.1101/824888
A UHPLC-HRMS based metabolomics and chemoinformatics approach to chemically distinguish ‘super foods’ from a variety of plant-based foods
10.1016/j.foodchem.2019.126071
Active nitrogen fixation by Crocosphaera expands their niche despite the presence of ammonium – A case study
10.1038/s41598-019-51378-4
Quantifying Oxygen Management and Temperature and Light Dependencies of Nitrogen Fixation by Crocosphaera watsonii
10.1128/msphere.00531-19
Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales
10.1016/j.ddmod.2019.08.012
Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree
10.1101/2020.05.04.077636
Reference data based insights expand understanding of human metabolomes
10.1101/2020.07.08.194159
Justin van der Hooft
van der Hooft Justin
/ Justin J.J. van der Hooft
ORCID: 0000-0002-9340-5511
Structural elucidation of low abundant metabolites in complex sample matrices
10.1007/s11306-013-0519-8
Non-smoky GLYCOSYLTRANSFERASE1 prevents the release of smoky aroma from tomato fruit
10.1105/tpc.113.114231
Automatic chemical structure annotation of an LC-MSn based metabolic profile from green tea
10.1021/ac400861a
Substructure-based annotation of high-resolution multistage MSn spectral trees
10.1002/rcm.6364
Structural annotation and elucidation of conjugated phenolic compounds in black, green, and white tea extracts
10.1021/jf300297y
Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake
10.1021/ac3017339
Spectral trees as a robust annotation tool in LC-MS based metabolomics
10.1007/s11306-011-0363-7
Metabolite identification using automated comparison of high-resolution multistage mass spectral trees
10.1021/ac2034216
Inhibitory activity of plumbagin produced by Drosera intermedia on food spoilage fungi
10.1002/jsfa.5522
A strategy for fast structural elucidation of metabolites in small volume plant extracts using automated MS-guided LC-MS-SPE-NMR
10.1002/mrc.2833
Thermal diffusivity of periderm from tomatoes of different maturity stages as determined by the concept of the frequency-domain open photoacoustic cell
10.1063/1.3530735
Polyphenol identification based on systematic and robust high-resolution accurate mass spectrometry fragmentation
10.1021/ac102546x
Iridoid and caffeoyl phenylethanoid glycosides of the endangered carnivorous plant Pinguicula lusitanica L. (Lentibulariaceae)
10.1016/j.bse.2009.05.003
Topic modeling for untargeted substructure exploration in metabolomics
10.1073/pnas.1608041113
Propagating annotations of molecular networks using in silico fragmentation
10.1371/journal.pcbi.1006089
Did a plant-herbivore arms race drive chemical diversity in Euphorbia?
10.1101/323014
Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa.
10.5702/massspectrometry.S0033
Interactions of blacktea polyphenols with human gut microbiota: implications for gut and cardiovascular health
10.3945/ajcn.113.058263
Identification of a drimenol synthase and drimenol oxidase from Persicaria hydropiper, involved in the biosynthesis of insect deterrent drimanes
10.1111/tpj.13527
Enhanced Acylcarnitine Annotation in High-Resolution Mass Spectrometry Data: Fragmentation Analysis for the Classification and Annotation of Acylcarnitines
10.3389/fbioe.2015.00026
Rapid and sustained systemic circulation of conjugated gut microbiol catabolites after single-dose black tea extract consumption
10.1021/pr5001253
In Silico Prediction and Automatic LC–MSn Annotation of Green Tea Metabolites in Urine
10.1021/ac403875b
Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose
10.1007/s11306-018-1438-5
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1101/463620
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
10.1101/491506
Accelerating metabolite identification in natural product research: toward an ideal combination of LC-HRMS/MS and NMR profiling, in silico databases and chemometrics
10.1021/acs.analchem.8b05112
Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages
10.1101/347716
Absorption, metabolism, distribution and excretion of (−)-epicatechin: A review of recent findings
https://doi.org/10.1016/j.mam.2017.11.002
Metabolite Identification in Complex Mixtures Using Nuclear Magnetic Resonance Spectroscopy
10.1007/978-3-319-28275-6_6-2
Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry
10.1093/bioinformatics/btx582
A comprehensive evaluation of the [2-14C](–)-epicatechin metabolome in rats
https://doi.org/10.1016/j.freeradbiomed.2016.08.001
The food metabolome: a window over dietary exposure
10.3945/ajcn.113.076133
Human studies on the absorption, distribution, metabolism, and excretion of tea polyphenols
10.3945/ajcn.113.058958
Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics
10.1021/acs.analchem.7b01391
A community-driven paired data platform to accelerate natural product mining by combining structural information from genomes and metabolomes
10.18174/FAIRdata2018.16286
Implementations of the chemical structural and compositional similarity metric in R and Python
10.1101/546150
Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1111/tpj.14292
A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters
10.1186/s13104-019-4222-3
The Metabolomics Society—Current State of the Membership and Future Directions
10.3390/metabo9050089
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
10.1039/C8FD00235E
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
10.1101/654459
Substantial extracellular metabolic differences found between phylogenetically closely related probiotic and pathogenic strains of Escherichia coli
10.3389/fmicb.2019.00252
Assessing specialized metabolite diversity in the cosmopolitan plant genus Euphorbia l.
10.3389/fpls.2019.00846
Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools
10.3390/metabo9070144
In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics
10.3390/metabo9100219
MIBiG 2.0: a repository for biosynthetic gene clusters of known function
10.1093/nar/gkz882
Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages
10.1016/j.foodchem.2019.125290
The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
10.1021/acscentsci.9b00806
Mass spectrometry searches using MASST
10.1038/s41587-019-0375-9
Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow
10.1016/j.phytochem.2020.112292
Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication
10.1126/sciadv.aax6328
Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree
10.1101/2020.05.04.077636
Linking genomics and metabolomics to chart specialized metabolic diversity
10.1039/D0CS00162G
Reproducible molecular networking of untargeted mass spectrometry data using GNPS
10.1038/s41596-020-0317-5
Decomposing metabolite set activity levels with PALS
10.1101/2020.06.07.138974
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1101/2020.06.12.148205
Phenylpropane as an Alternative Dearomatizing Unit of Indoles: Discovery of Inaequalisines A and B Using Substructure-Informed Molecular Networking
10.1021/acs.orglett.0c02153
matchms - processing and similarity evaluation of mass spectrometry data
10.1101/2020.08.06.239244
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
10.1101/2020.08.11.245928
BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters
10.1101/2020.08.17.240838
matchms - processing and similarity evaluation of mass spectrometry data.
10.21105/joss.02411
ReDU: a framework to find and reanalyze public mass spectrometry data
10.1038/s41592-020-0916-7
Feature-based molecular networking in the GNPS analysis environment
10.1038/s41592-020-0933-6
Rapid Development of Improved Data-dependent Acquisition Strategies
10.1101/2020.09.11.293092
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree
10.1038/s41589-020-00677-3
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data
10.1038/s41587-020-0700-3
The ant fungus garden acts as an external digestive system
10.1101/2020.11.18.389361
BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
10.1101/2020.12.14.422671
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters
10.1093/gigascience/giaa154
Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs
10.1371/journal.ppat.1008932
Comparative Metabologenomics Analysis of Polar Actinomycetes
10.3390/md19020103
Ranking Metabolite Sets by Their Activity Levels
10.3390/metabo11020103
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
10.1371/journal.pcbi.1008724
Rapid Development of Improved Data-Dependent Acquisition Strategies
10.1021/acs.analchem.0c03895
MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons
10.1101/2021.04.18.440324
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
10.1371/journal.pcbi.1008920
Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview
10.3390/metabo11070445
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden
10.1128/mSystems.00601-21
Comprehensive Large-Scale Integrative Analysis of Omics Data To Accelerate Specialized Metabolite Discovery
10.1128/mSystems.00726-21
Kai Dührkop
Dührkop Kai
ORCID: 0000-0002-9056-0540
Significance estimation for large scale metabolomics annotations by spectral matching
10.1038/s41467-017-01318-5
Searching molecular structure databases with tandem mass spectra using CSI:FingerID
10.1073/pnas.1509788112
Fragmentation trees reloaded
10.1007/978-3-319-16706-0_10
Critical Assessment of Small Molecule Identification 2016: automated methods
10.1186/s13321-017-0207-1
Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints
10.1093/bioinformatics/bty245
Faster mass decomposition
10.1007/978-3-642-40453-5_5
Speedy colorful subtrees
10.1007/978-3-319-21398-9_25
Fragmentation trees reloaded
10.1186/s13321-016-0116-8
Heuristic algorithms for the Maximum Colorful Subtree problem
10.4230/LIPIcs.WABI.2018.23
Metabolite identification through multiple kernel learning on fragmentation trees
10.1093/bioinformatics/btu275
Fast metabolite identification with Input Output Kernel Regression
10.1093/bioinformatics/btw246
Fast alignment of fragmentation trees
10.1093/bioinformatics/bts207
Current challenges in plant Eco-Metabolomics
10.3390/ijms19051385
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
10.1038/s41592-019-0344-8
Feature-based Molecular Networking in the GNPS Analysis Environment
10.1101/812404
Computational methods for small molecule identification
10.1515/itit-2019-0033
ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules
10.1101/842740
Classes for the masses: Systematic classification of unknowns using fragmentation spectra
10.1101/2020.04.17.046672
Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree
10.1101/2020.05.04.077636
Feature-based molecular networking in the GNPS analysis environment
10.1038/s41592-020-0933-6
Database-independent molecular formula annotation using Gibbs sampling through ZODIAC
10.1038/s42256-020-00234-6
Publisher Correction: Database-independent molecular formula annotation using Gibbs sampling through ZODIAC
10.1038/s42256-020-00259-x
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree
10.1038/s41589-020-00677-3
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
10.1038/s41587-020-0740-8
Assigning confidence to structural annotations from mass spectra with COSMIC
10.1101/2021.03.18.435634
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment
10.1038/s41467-021-23953-9
MSNovelist: De novo structure generation from mass spectra
10.1101/2021.07.06.450875
Madeleine Ernst
Ernst Madeleine
ORCID: 0000-0001-9530-3837
A metabolomic protocol for plant systematics by matrix-assisted laser-desorption/ionization time-of flight mass spectrometry
10.1016/j.aca.2015.01.002
Mass spectrometry in plant metabolomics strategies: From analytical platforms to data acquisition and processing
10.1039/c3np70086k
Mass Spectrometry of flavonoid vicenin-2, based sunlight barriers in Lychnophora species
10.1038/srep04309
Global medicinal uses of Euphorbia L. (Euphorbiaceae)
10.1016/j.jep.2015.10.025
A phylogenetic road map to antimalarial Artemisia species.
10.1016/j.jep.2018.06.030
Using evolutionary tools to search for novel psychoactive plants
10.1017/S1479262116000344
Updates on the genus Euphorbia (Euphorbiaceae) in Santa Catarina, Brazil
0.11646/phytotaxa.298.3.2
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
10.1039/C8FD00235E
Implementations of the chemical structural and compositional similarity metric in R and Python
10.1101/546150
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
10.3390/metabo9070144
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1111/tpj.14292
Feature-based Molecular Networking in the GNPS Analysis Environment
10.1101/812404
Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data
10.1101/750471
Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS
10.1101/2020.01.13.905091
Reproducible Molecular Networking Of Untargeted Mass Spectrometry Data Using GNPS.
10.26434/chemrxiv.9333212.v1
Gestational-age-dependent development of the neonatal metabolome
10.1101/2020.03.27.20045534
Untargeted metabolomic study of autism in newborn screening samples: a pilot study
10.1101/2020.04.17.20069153
Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree
10.1101/2020.05.04.077636
Thapsigargins and induced chemical defence in Thapsia garganica
10.1007/s00049-020-00315-3
The ant fungus garden acts as an external digestive system
10.1101/2020.11.18.389361
Discovery of Urinary Biomarkers of Seaweed Intake Using Untargeted LC–MS Metabolomics in a Three-Way Cross-Over Human Study
10.3390/metabo11010011
Combined Urinary Biomarkers to Assess Coffee Intake Using Untargeted Metabolomics: Discovery in Three Pilot Human Intervention Studies and Validation in Cross-Sectional Studies
10.1021/acs.jafc.1c01155
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden
10.1128/mSystems.00601-21
