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Metabolite identification using automated comparison of high-resolution multistage mass spectral trees

Rojas-Cherto M.; Peironcely J.E.; Kasper P.T.; Hooft J.J.J van der.; Vos R.C.H. de; Vreeken R.J.; Hankemeier T.; Reijmers T.H.

Analytical Chemistry, 2012

https://doi.org/10.1021/ac2034216

Thomas Hankemeier

Hankemeier Thomas

ORCID: 0000-0001-7871-2073

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Weight loss moderately affects the mixed meal challenge response of the plasma metabolome and transcriptome of peripheral blood mononuclear cells in abdominally obese subjects 10.1007/s11306-018-1328-x

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Pharmacometabolomics Informs about pharmacokinetic profile of Methylphenidate 10.1002/psp4.12309

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Towards Standards for Human Fecal Sample Preparation in Targeted and Untargeted LC-HRMS Studies 10.3390/metabo11060364

Purine Pathway Implicated in Mechanism of Resistance to Aspirin Therapy: Pharmacometabolomics-Informed Pharmacogenomics 10.1038/clpt.2013.119

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Effects of Metformin on Metabolite Profiles and LDL Cholesterol in Patients With Type 2 Diabetes 10.2337/dc15-0658

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Assessing the metabolic effects of prednisolone in healthy volunteers using urine metabolic profiling 10.1186/gm395

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Stable Single-Walled Carbon Nanotube-Streptavidin Complex for Biorecognition 10.1021/jp911441d

The effect of preanalytical factors on stability of the proteome and selected metabolites in cerebrospinal fluid (CSF) 10.1021/pr9005876

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Integration of pharmacometabolomics with pharmacokinetics and pharmacodynamics: towards personalized drug therapy: an addition to the topical collection "Recent Advances in Pharmacometabolomics: Enabling Tools for Precision Medicine" 10.1007/s11306-017-1189-8

p53 attenuates AKT signaling by modulating membrane phospholipid composition 10.18632/oncotarget.4067

Alkaloid profiling of the Chinese herbal medicine Fuzi by combination of matrix-assisted laser desorption ionization mass spectrometry with liquid chromatography-mass spectrometry 10.1016/j.chroma.2008.11.077

Traditional processing strongly affects metabolite composition by hydrolysis in Rehmannia glutinosa Roots 10.1248/cpb.59.546

Metabolic risks of neonates at birth following in utero exposure to HIV-ART: the amino acid profile of cord blood 10.1007/s11306-017-1222-y

Exome-sequencing in a large population-based study reveals a rare Asn396Ser variant in the LIPG gene associated with depressive symptoms 10.1038/mp.2016.101

Quantitative Proteomics and Metabolomics Analysis of Normal Human Cerebrospinal Fluid Samples 10.1074/mcp.M110.000877

LC/MS analysis of stratum corneum lipids: ceramide profiling and discovery 10.1194/jlr.M014456

Analytical strategies in lipidomics and applications in disease biomarker discovery 10.1016/j.jchromb.2009.01.038

A new approach to untargeted integration of high resolution liquid chromatography-mass spectrometry data 10.1016/j.aca.2013.09.028

Online capillary liquid-liquid electroextraction of peptides as fast pre-concentration prior to LC-MS 10.1002/elps.201000347

Systems Biology-Based Diagnostic Principles as Pillars of the Bridge between Chinese and Western Medicine 10.1055/s-0030-1250450

Equating, or correction for between-block effects with application to body fluid LC-MS and NMR metabolomics data sets 10.1021/ac902346a

Comprehensive metabolomics to evaluate the impact of industrial processing on the phytochemical composition of vegetable purees 10.1016/j.foodchem.2014.07.076

Characterization of the therapeutic properties of Chinese herbal materials by measuring delayed luminescence and dendritic cell-based immunomodulatory response 10.1016/j.jphotobiol.2017.01.018

On-line large-volume electroextraction coupled to liquid chromatography-mass spectrometry to improve detection of peptides 10.1016/j.chroma.2012.06.016

Microfluidic titer plate for stratified 3D cell culture 10.1039/c3lc50210d

Systems toxicology study of doxorubicin on rats using ultra performance liquid chromatography coupled with mass spectrometry based metabolomics 10.1007/s11306-009-0165-3

Feasibility of electrodialysis as a fast and selective sample preparation method for the profiling of low-abundant peptides in biofluids 10.1002/elps.200800500

Comprehensive LC-MSE Lipidomic Analysis using a Shotgun Approach and Its Application to Biomarker Detection and Identification in Osteoarthritis Patients 10.1021/pr901094j

Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research 10.1007/s11306-009-0168-0

Tunable Ionic Mobility Filter for Depletion Zone Isotachophoresis 10.1021/ac301612n

Single-electrolyte isotachophoresis using a nanochannel-induced depletion zone 10.1021/ac2018348

Expanding and understanding metabolite space 10.1186/1758-2946-2-S1-P39

OMG: Open Molecule Generator 10.1186/1758-2946-4-21

Metabolite profiling of small cerebrospinal fluid sample volumes with gas chromatography-mass spectrometry: application to a rat model of multiple sclerosis 10.1007/s11306-012-0428-2

How Do Metabolites Differ from Their Parent Molecules and How Are They Excreted? 10.1021/ci300487z

Localization of fatty acyl and double bond positions in phosphatidylcholines using a dual stage CID fragmentation coupled with ion mobility mass spectrometry 10.1007/s13361-011-0172-2

The impact of delayed storage on the measured proteome and metabolome of human cerebrospinal fluid 10.1373/clinchem.2011.167601

Solvent Exchange Module for LC-NMR Hyphenation Using Machine Vision-Controlled Droplet Evaporation 10.1021/ac401068j

Elastomeric microvalves as tunable nanochannels for concentration polarization 10.1039/c3lc50658d

Genome-wide pleiotropy of adult aggression and blood metabolites 10.1007/s10519-016-9812-4

Metabolomic and transcriptomic profiling of adult mice and larval zebrafish leptin mutants reveal a common pattern of changes in metabolites and signaling pathways 10.1186/s13578-021-00642-0

Rob Vreeken

Vreeken Rob / Rob Vreeken

ORCID: 0000-0003-3568-1371

Potent peptidic fusion inhibitors of influenza virus 10.1126/science.aan0516

Mass spectrometric recommendations for Quan/Qual analysis using liquid-chromatography coupled to quadrupole time-of-flight mass spectrometry 10.1016/j.aca.2018.02.055

The pipelined metabolite identification based on MS fragmentation. 10.1186/1758-2946-2-s1-p53

Comprehensive LC-MS E lipidomic analysis using a shotgun approach and its application to biomarker detection and identification in osteoarthritis patients. 10.1021/pr901094j

The effect of preanalytical factors on stability of the proteome and selected metabolites in cerebrospinal fluid (CSF). 10.1021/pr9005876

Liquid chromatography with triple-quadrupole and quadrupole-time-of-flight mass spectrometry for the determination of micro-constituents - a comparison. 10.1007/s00216-003-2485-x

Generic solid phase extraction-liquid chromatography-tandem mass spectrometry method for fast determination of drugs in biological fluids. 10.1016/s1570-0232(02)01013-9

Determination of oxytetracycline and its degradation products by high-performance liquid chromatography-tandem mass spectrometry in manure-containing anaerobic test systems. 10.1016/s1570-0232(02)00468-3

Determination of polar organophosphorus pesticides in aqueous samples by direct injection using liquid chromatography-tandem mass spectrometry. 10.1016/s0021-9673(01)00660-4

Capillary electrochromatography/nanoelectrospray mass spectrometry for attomole characterization of peptides. 10.1002/1097-0231(20000830)14:16<1448::aid-rcm44>3.0.co;2-9

Determination of daminozide in apples and apple leaves by liquid chromatography--mass spectrometry. 10.1016/s0021-9673(98)00915-7

Rapid target analysis of microcontaminants in water by on-line single-short-column liquid chromatography combined with atmospheric pressure chemical ionization tandem mass spectrometry. 10.1016/s0021-9673(97)00558-x

On-line post-column Diels-Alder derivatization for the determination of vitamin D3 and its metabolites by liquid chromatography/thermospray mass spectrometry. 10.1002/bms.1200221102

Evaluation of eluents in thermospray liquid chromatography-mass spectrometry for identification and determination of pesticides in environmental samples. 10.1016/s0021-9673(01)88502-2

Deregulation of secondary metabolism in a histone deacetylase mutant of Penicillium chrysogenum. 10.1002/mbo3.598

Integration of Ion Mobility MSE after Fully Automated, Online, High-Resolution Liquid Extraction Surface Analysis Micro-Liquid Chromatography. 10.1021/acs.analchem.7b03512

High sensitivity and selectivity in quantitative analysis of drugs in biological samples using 4-column multidimensional micro-UHPLC-MS enabling enhanced sample loading capacity. 10.1016/j.aca.2017.07.067

Fetal Metabolic Stress Disrupts Immune Homeostasis and Induces Proinflammatory Responses in Human Immunodeficiency Virus Type 1- and Combination Antiretroviral Therapy-Exposed Infants. 10.1093/infdis/jix291

Altered expression of epidermal lipid bio-synthesis enzymes in atopic dermatitis skin is accompanied by changes in stratum corneum lipid composition. 10.1016/j.jdermsci.2017.05.005

Endometriosis is associated with aberrant metabolite profiles in plasma. 10.1016/j.fertnstert.2016.12.032

Quantitative analysis of ceramides using a novel lipidomics approach with three dimensional response modelling. 10.1016/j.bbalip.2016.07.004

Metabolomics profiling of the free and total oxidised lipids in urine by LC-MS/MS: application in patients with rheumatoid arthritis. 10.1007/s00216-016-9742-2

Metabolic characterization of the natural progression of chronic hepatitis B. 10.1186/s13073-016-0318-8

Serum-Based Oxylipins Are Associated with Outcomes in Primary Prevention Implantable Cardioverter Defibrillator Patients. 10.1371/journal.pone.0157035

Identification of a Polyketide Synthase Involved in Sorbicillin Biosynthesis by Penicillium chrysogenum. 10.1128/aem.00350-16

Enhanced performance for the analysis of prostaglandins and thromboxanes by liquid chromatography-tandem mass spectrometry using a new atmospheric pressure ionization source. 10.1016/j.chroma.2016.02.055

Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum. 10.1186/s12864-015-2154-4

Collagen Induced Arthritis in DBA/1J Mice Associates with Oxylipin Changes in Plasma. 10.1155/2015/543541

First-Trimester Serum Acylcarnitine Levels to Predict Preeclampsia: A Metabolomics Approach. 10.1155/2015/857108

Matrix Effect Compensation in Small-Molecule Profiling for an LC-TOF Platform Using Multicomponent Postcolumn Infusion. 10.1021/ac504268y

Modulation of stratum corneum lipid composition and organization of human skin equivalents by specific medium supplements. 10.1111/exd.12740

A mutasynthesis approach with a Penicillium chrysogenum ΔroqA strain yields new roquefortine D analogues. 10.1002/cbic.201402686

Testing tuberculosis drug efficacy in a zebrafish high-throughput translational medicine screen. 10.1128/aac.03588-14

Roux-en-Y gastric bypass surgery, but not calorie restriction, reduces plasma branched-chain amino acids in obese women independent of weight loss or the presence of type 2 diabetes. 10.2337/dc14-0195

Gas pressure assisted microliquid-liquid extraction coupled online to direct infusion mass spectrometry: a new automated screening platform for bioanalysis. 10.1021/ac502582f

Metabolic phenotyping reveals a lipid mediator response to ionizing radiation. 10.1021/pr5005295

Comprehensive metabolomics to evaluate the impact of industrial processing on the phytochemical composition of vegetable purees. 10.1016/j.foodchem.2014.07.076

Pharmacometabolomics reveals that serotonin is implicated in aspirin response variability. 10.1038/psp.2014.22

Enhanced lipid isomer separation in human plasma using reversed-phase UPLC with ion-mobility/high-resolution MS detection. 10.1194/jlr.d047795

A non-canonical NRPS is involved in the synthesis of fungisporin and related hydrophobic cyclic tetrapeptides in Penicillium chrysogenum. 10.1371/journal.pone.0098212

Metabolomics profiling for identification of novel potential markers in early prediction of preeclampsia. 10.1371/journal.pone.0098540

A protective lipidomic biosignature associated with a balanced omega-6/omega-3 ratio in fat-1 transgenic mice. 10.1371/journal.pone.0096221

Integrating metabolomics profiling measurements across multiple biobanks. 10.1021/ac404191a

Transient inflammatory-like state and microbial dysbiosis are pivotal in establishment of mucosal homeostasis during colonisation of germ-free mice. 10.3920/bm2013.0018

The importance of free fatty acid chain length for the skin barrier function in atopic eczema patients. 10.1111/exd.12293

Intercellular skin barrier lipid composition and organization in Netherton syndrome patients. 10.1038/jid.2013.517

Novel key metabolites reveal further branching of the roquefortine/meleagrin biosynthetic pathway. 10.1074/jbc.m113.512665

Postprandial fatty acid specific changes in circulating oxylipins in lean and obese men after high-fat challenge tests. 10.1002/mnfr.201300321

Combined LC/MS-platform for analysis of all major stratum corneum lipids, and the profiling of skin substitutes. 10.1016/j.bbalip.2013.10.002

Three-phase electroextraction: a new (online) sample purification and enrichment method for bioanalysis. 10.1021/ac4010716

A branched biosynthetic pathway is involved in production of roquefortine and related compounds in Penicillium chrysogenum. 10.1371/journal.pone.0065328

Skin barrier dysfunction in non-lesional atopic eczema: the role of stratum corneum lipids. 10.1684/ejd.2013.1973

Lipidomics of familial longevity. 10.1111/acel.12064

Plasma oxylipin profiling identifies polyunsaturated vicinal diols as responsive to arachidonic acid and docosahexaenoic acid intake in growing piglets. 10.1194/jlr.m034918

Automated pipeline for de novo metabolite identification using mass-spectrometry-based metabolomics. 10.1021/ac303218u

Gender-dependent associations of metabolite profiles and body fat distribution in a healthy population with central obesity: towards metabolomics diagnostics. 10.1089/omi.2012.0062

Fragmentation trees for the structural characterisation of metabolites. 10.1002/rcm.6340

Increase in short-chain ceramides correlates with an altered lipid organization and decreased barrier function in atopic eczema patients. 10.1194/jlr.p030338

Increased presence of monounsaturated fatty acids in the stratum corneum of human skin equivalents. 10.1038/jid.2012.262

Quantitative profiling of oxylipins through comprehensive LC-MS/MS analysis: application in cardiac surgery. 10.1007/s00216-012-6226-x

Metabolite identification using automated comparison of high-resolution multistage mass spectral trees. 10.1021/ac2034216

A lipidomic analysis approach to evaluate the response to cholesterol-lowering food intake. 10.1007/s11306-011-0384-2

An efficient hydrophilic interaction liquid chromatography separation of 7 phospholipid classes based on a diol column. 10.1016/j.chroma.2011.11.034

The impact of delayed storage on the measured proteome and metabolome of human cerebrospinal fluid. 10.1373/clinchem.2011.167601

Attenuation of Slc27a5 gene expression followed by LC-MS measurement of bile acid reconjugation using metabolomics and a stable isotope tracer strategy. 10.1021/pr200475g

Anacetrapib promotes reverse cholesterol transport and bulk cholesterol excretion in Syrian golden hamsters. 10.1194/jlr.m016410

Identifying static and kinetic lipid phenotypes by high resolution UPLC-MS: unraveling diet-induced changes in lipid homeostasis by coupling metabolomics and fluxomics. 10.1021/pr200480g

Elemental composition determination based on MS(n). 10.1093/bioinformatics/btr409

Lamellar lipid organization and ceramide composition in the stratum corneum of patients with atopic eczema. 10.1038/jid.2011.175

Localization of fatty acyl and double bond positions in phosphatidylcholines using a dual stage CID fragmentation coupled with ion mobility mass spectrometry. 10.1007/s13361-011-0172-2

Metabolomics of cerebrospinal fluid reveals changes in the central nervous system metabolism in a rat model of multiple sclerosis. 10.1007/s11306-011-0306-3

LC/MS analysis of stratum corneum lipids: ceramide profiling and discovery. 10.1194/jlr.m014456

The pharmacokinetics and pharmacological effect of (S)-5-OH-DPAT following controlled delivery with transdermal iontophoresis. 10.1002/jps.22492

In vivo D2O labeling to quantify static and dynamic changes in cholesterol and cholesterol esters by high resolution LC/MS. 10.1194/jlr.d009787

Mass spectrometric analysis of intact human monoclonal antibody aggregates fractionated by size-exclusion chromatography. 10.1007/s11095-010-0224-5

Coupling of column liquid chromatography and thermospray mass spectrometry via phase‐system switching with an ion‐exchange trapping column 10.1002/bms.1200210607

Membrane interface for the direct coupling of pyrolysis and mass spectrometry 10.1016/0003-2670(95)00244-T

Nonpolar solvents for normal-phase liquid chromatography and postcolumn extraction in thermospray liquid chromatography/mass spectrometry 10.1021/ac00214a033

The derivatization of fatty acids by (chloro)alkyl chloroformates in non‐aqueous and aqueous media for GC analysis 10.1002/jhrc.1240151203

Coupling of ion-pair liquid chromatography and thermospray mass spectrometry via phase-system switching with a polymeric trapping column 10.1016/0021-9673(93)83065-Z

Coupling of capillary zone electrophoresis to mass spectrometry (MS and MS/MS) via a nanoelectrospray interface for the characterisation of some β-agonists 10.1002/(SICI)1097-0231(19990415)13:7<612::AID-RCM531>3.0.CO;2-D

Capillary electrochromatography/nanoelectrospray mass spectrometry for attomole characterization of peptides 10.1002/1097-0231(20000830)14:16<1448::AID-RCM44>3.0.CO;2-9

Determination of quaternary amine pesticides by thermospray mass spectrometry 10.1016/0021-9673(93)83407-J

Advance in Analysis and Detection Technologies for Phospholipidomics 10.1016/S1872-2040(16)60939-8

Recent developments in sample-pretreatment techniques for mass spectrometry-based metabolomics 10.1016/j.trac.2014.06.003

The influence of citrate, EDTA, and heparin anticoagulants to human plasma LC-MS lipidomic profiling 10.1007/s11306-012-0450-4

Chapter 11. On-Line Post Column Liquid-Solid and Liquid-Liquid Extractions in Environmental Liquid Chromatography- Thermospray-Mass Spectrometry 10.1016/S0301-4770(08)60788-5

The use of mobile phase additives in the determination of 55 (polar) pesticides by column liquid chromatography-thermospray-mass spectrometry 10.1080/03067319408033093

Ion trap mass spectrometry as detector for capillary electrochromatography of peptides: Possibilities and limitations 10.1002/mcs.1049

Global profiling of the muscle metabolome: method optimization, validation and application to determine exercise-induced metabolic effects 10.1007/s11306-014-0701-7

Erratum: Localization of fatty acyl and double bond positions in phosphatidylcholines using a dual stage CID fragmentation coupled with ion mobility mass spectrometry (Journal of The American Society for Mass Spectrometry DOI: 10.1007/s13361-011-0172-2) 10.1007/s13361-011-0199-4

Selective analysis of the herbicides glyphosate and aminomethylphosphonic acid in water by on-line solid-phase extraction-high- performance liquid chromatography-electrospray ionization mass spectrometry 10.1016/S0021-9673(97)01129-1

Erratum: Comprehensive LC-MS^Elipidomic analysis using a shotgun approach and its application to biomarker detection and identification in osteoarthritis patients (Journal of Proteome Research (2010) 9 (2377-2389) DOI: 10.1021/pr901094j) 10.1021/pr200420k

Chloroacetonitrile as eluent additive in thermospray liquid chromatography/negative ion mass spectrometry for the characterization of chlorinated organic pollutants 10.1002/bms.1200190806

Rapid metabolic screening of early zebrafish embryogenesis based on direct infusion-nanoESI-FTMS 10.1007/s11306-012-0493-6

Identification of Artefacts in the Desorption of Active Charcoal Tubes with Carbon Disulphide and Methanol. Reduction of Artefact Formation by Selecting Other Polar Additives 10.1080/03067318808079927

Ionisation efficiencies can be predicted in complicated biological matrices: A proof of concept 10.1016/j.aca.2018.05.072

Cross-Species Molecular Imaging of Bile Salts and Lipids in Liver: Identification of Molecular Structural Markers in Health and Disease 10.1021/acs.analchem.8b01378

Targeted Drug and Metabolite Imaging: Desorption Electrospray Ionization Combined with Triple Quadrupole Mass Spectrometry 10.1021/acs.analchem.8b03857

Development and evaluation of matrix application techniques for high throughput mass spectrometry imaging of tissues in the clinic 10.1016/j.clinms.2019.01.004

Oxylipin profiling in endothelial cells in vitro – Effects of DHA and hydrocortisone upon an inflammatory challenge 10.1016/j.prostaglandins.2019.106352

Quantitative Mass Spectrometry Imaging to Study Drug Distribution in the Intestine Following Oral Dosing 10.1021/acs.analchem.0c03956

Quantitative mass spectrometry imaging of drugs and metabolites: a multiplatform comparison 10.1007/s00216-021-03210-0

Direct nose to brain delivery of small molecules: critical analysis of data from a standardized in vivo screening model in rats. 10.1080/10717544.2020.1837291

2-Methyl-pentanoyl-carnitine (2-MPC): a urine biomarker for patent Ascaris lumbricoides infection. 10.1038/s41598-020-72804-y

Skin of atopic dermatitis patients shows disturbed β-glucocerebrosidase and acid sphingomyelinase activity that relates to changes in stratum corneum lipid composition. 10.1016/j.bbalip.2020.158673

Spatial heterogeneity of nanomedicine investigated by multiscale imaging of the drug, the nanoparticle and the tumour environment. 10.7150/thno.38625

Infrared ion spectroscopy: New opportunities for small-molecule identification in mass spectrometry - A tutorial perspective. 10.1016/j.aca.2019.10.043

Enhanced Sensitivity Using MALDI Imaging Coupled with Laser Postionization (MALDI-2) for Pharmaceutical Research. 10.1021/acs.analchem.9b02495

Oxidative stress and abnormal bioactive lipids in early cystic fibrosis lung disease. 10.1016/j.jcf.2019.04.011

High-Resolution Mass Spectrometry Quantification: Impact of Differences in Data Processing of Centroid and Continuum Data. 10.1007/s13361-018-2101-0

Translational safety biomarkers of colonic barrier integrity in the rat. 10.1002/jat.3639

Evaluation of cardiac arrhythmic risks using a rabbit model of left ventricular systolic dysfunction. 10.1016/j.ejphar.2018.05.026

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