Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
Wout Bittremieux
Christopher Chen
Pieter C. Dorrestein
Emma L. Schymanski
Tobias Schulze
Steffen Neumann
Rene Meier
Simon Rogers
Mingxun Wang
Mingxun Wang
Wang Mingxun
/ Ming
ORCID: 0000-0001-7647-6097
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
10.1038/nbt.3597
Detection of Ovarian Cancer Using Samples Sourced from the Vaginal Microenvironment
10.1101/597740
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
10.1101/654459
Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data
10.1101/750471
Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure
10.1101/804401
Protocol for community‐created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure
10.1002/rcm.8725
Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
10.1101/2020.05.09.086066
Ion Identity Molecular Networking in the GNPS Environment
10.1101/2020.05.11.088948
ReDU: a framework to find and reanalyze public mass spectrometry data
10.1038/s41592-020-0916-7
The ant fungus garden acts as an external digestive system
10.1101/2020.11.18.389361
A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria
10.3390/md19010020
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment
10.1038/s41467-021-23953-9
Quick-start infrastructure for untargeted metabolomics analysis in GNPS
10.1038/s42255-021-00429-0
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden
10.1128/mSystems.00601-21
A Synthesis-Based Reverse Metabolomics Approach for the Discovery of Chemical Structures from Humans and Animals.
10.21203/rs.3.rs-820302/v1
Native Metabolomics Identifies the Rivulariapeptolide Family of Protease Inhibitors
10.1101/2021.09.03.458897
Emma Schymanski
Schymanski Emma
/ Emma Craven (pre 2005)
ORCID: 0000-0001-6868-8145
Discovering pesticides and their TPs in Luxembourg waters using open cheminformatics approaches
10.1016/j.envint.2021.106885
SPLASH, a hashed identifier for mass spectra
10.1038/nbt.3689
Small Molecule Identification with MOLGEN and Mass Spectrometry
10.3390/metabo3020440
CASMI: And the Winner is . . .
10.3390/metabo3020412
Mathematical Chemistry and Chemoinformatics
10.1515/9783110254075
The Critical Assessment of Small Molecule Identification (CASMI): Challenges and Solutions
10.3390/metabo3030517
Multicriteria Approach To Select Polyaromatic River Mutagen Candidates
10.1021/es503640k
Solving CASMI 2013 with MetFrag, MetFusion and MOLGEN-MS/MS
10.5702/massspectrometry.s0036
Computer Tools for Structure Elucidation in Effect-Directed Analysis
10.1007/978-3-642-18384-3_8
Biotransformation of Benzotriazoles: Insights from Transformation Product Identification and Compound-Specific Isotope Analysis
10.1021/es405694z
Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence
10.1021/es5002105
Prioritizing Unknown Transformation Products from Biologically-Treated Wastewater Using High-Resolution Mass Spectrometry, Multivariate Statistics, and Metabolic Logic
10.1021/acs.analchem.5b02905
Exploring the Behaviour of Emerging Contaminants in the Water Cycle using the Capabilities of High Resolution Mass Spectrometry
10.2533/chimia.2014.793
Suspect and nontarget screening approaches to identify organic contaminant records in lake sediments
10.1007/s00216-014-8166-0
Integrated biological–chemical approach for the isolation and selection of polyaromatic mutagens in surface waters
10.1007/s00216-013-7349-4
MetFrag relaunched: incorporating strategies beyond in silico fragmentation
10.1186/s13321-016-0115-9
Systematic Exploration of Biotransformation Reactions of Amine-Containing Micropollutants in Activated Sludge
10.1021/acs.est.5b05186
Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go?
10.4155/bio-2016-0244
Strategies to Characterize Polar Organic Contamination in Wastewater: Exploring the Capability of High Resolution Mass Spectrometry
10.1021/es4044374
Metabolite identification: are you sure? And how do your peers gauge your confidence?
10.1007/s11306-014-0656-8
Statistical Approaches for LC-HRMS Data To Characterize, Prioritize, and Identify Transformation Products from Water Treatment Processes
10.1021/bk-2016-1241.ch004
Extended Suspect and Non-Target Strategies to Characterize Emerging Polar Organic Contaminants in Raw Wastewater with LC-HRMS/MS
10.1021/acs.est.5b03454
Mass spectral databases for LC/MS- and GC/MS-based metabolomics: State of the field and future prospects
10.1016/j.trac.2015.09.005
The use of MS classifiers and structure generation to assist in the identification of unknowns in effect-directed analysis
10.1016/j.aca.2008.03.060
Critical Assessment of Small Molecule Identification 2016: automated methods
10.1186/s13321-017-0207-1
Open Science for Identifying “Known Unknown” Chemicals
10.1021/acs.est.7b01908
Nontarget Screening with High Resolution Mass Spectrometry in the Environment: Ready to Go?
10.1021/acs.est.7b02184
Dark matter in host-microbiome metabolomics: Tackling the unknowns–A review
10.1016/j.aca.2017.12.034
Annotating Nontargeted LC-HRMS/MS Data with Two Complementary Tandem Mass Spectral Libraries
10.3390/metabo9010003
Supporting non-target identification by adding hydrogen deuterium exchange MS/MS capabilities to MetFrag
10.1007/s00216-019-01885-0
Nontarget Screening Reveals Time Trends of Polar Micropollutants in a Riverbank Filtration System
10.1021/acs.est.9b01750
Connecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges
10.1039/C9EM00068B
The metaRbolomics Toolbox in Bioconductor and beyond
10.3390/metabo9100200
Exploring open cheminformatics approaches for categorizing per- and polyfluoroalkyl substances (PFASs)
10.1039/C9EM00321E
Evaluation of reverse osmosis drinking water treatment of riverbank filtrate using bioanalytical tools and non-target screening
10.1039/C9EW00741E
The exposome and health: Where chemistry meets biology
10.1126/science.aay3164
Tracking complex mixtures of chemicals in our changing environment
10.1126/science.aay6636
Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
10.1101/2020.05.09.086066
Patroon: Open Source Software Platform for Environmental Mass Spectrometry Based Non-target Screening
10.21203/rs.3.rs-36675/v1
patRoon: Open source software platform for environmental mass spectrometry based non-target screening
10.21203/rs.3.rs-36675/v2
Studying Charge Migration Fragmentation of Sodiated Precursor Ions in Collision-Induced Dissociation at the Library Scale
10.1021/jasms.0c00240
Empowering Large Chemical Knowledge Bases for Exposomics: Pubchemlite Meets Metfrag
10.21203/rs.3.rs-107432/v1
Improving Target and Suspect Screening High-Resolution Mass Spectrometry Workflows in Environmental Analysis by Ion Mobility Separation
10.1021/acs.est.0c05713
patRoon: open source software platform for environmental mass spectrometry based non-target screening
10.1186/s13321-020-00477-w
Non-target screening with high-resolution mass spectrometry: critical review using a collaborative trial on water analysis
10.1007/s00216-015-8681-7
Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas
10.3390/metabo8030051
“MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies
10.1186/s13321-018-0299-2
Expanding the Use of Spectral Libraries in Proteomics
10.1021/acs.jproteome.8b00485
Effect-directed analysis supporting monitoring of aquatic environments — An in-depth overview
10.1016/j.scitotenv.2015.11.102
An ecotoxicological view on neurotoxicity assessment
10.1186/s12302-018-0173-x
A European proposal for quality control and quality assurance of tandem mass spectral libraries
10.1186/s12302-020-00314-9
Exploring the Potential of a Global Emerging Contaminant Early Warning Network through the Use of Retrospective Suspect Screening with High-Resolution Mass Spectrometry
10.1021/acs.est.8b00365
Similarity of High-Resolution Tandem Mass Spectrometry Spectra of Structurally Related Micropollutants and Transformation Products
10.1007/s13361-017-1797-6
The NORMAN Association and the European Partnership for Chemicals Risk Assessment (PARC): let’s cooperate!
10.1186/s12302-020-00375-w
Correlation between Solution and the Solid State: The pH Dependent Composition in the Ternary System [Co(H2O)6]2+ or [Ni(H2O)6]2+/Piperazine/Phosphate
10.1002/zaac.200390031
Mining the NIST Mass Spectral Library Reveals the Extent of Sodium Assisted Inductive Cleavage in Collision-Induced Fragmentation
10.26434/chemrxiv.12114987.v1
Thallium(I) complexes with modified poly(pyrazolyl)borate ligands—metal-ligand coordination and crystal packing
10.1016/S0277-5387(01)01026-9
Retention projection enables accurate calculation of liquid chromatographic retention times across labs and methods
10.1016/j.chroma.2015.07.108
Retrospective Non-target Analysis to Support Regulatory Water Monitoring: From Masses of Interest to Recommendations via in silico workflows
10.21203/rs.3.rs-136443/v1
Synthesis, Structure and Solution Chemistry of (5, 5′-Dimethyl-2, 2′-bipyridine)(IDA)copper(II) and Structural Comparison With Aqua(IDA)(1, 10-phenanthroline)copper(II) (IDA = iminodiacetato)
10.1002/zaac.200300223
Future water quality monitoring — Adapting tools to deal with mixtures of pollutants in water resource management
10.1016/j.scitotenv.2014.12.057
Nontarget Analysis of Environmental Samples Based on Liquid Chromatography Coupled to High Resolution Mass Spectrometry (LC-HRMS)
10.1016/bs.coac.2016.01.012
Recent analytical methods for risk assessment of emerging contaminants in ecosystems
10.1016/B978-0-12-809582-9.00014-1
Expanded coverage of non-targeted LC-HRMS using atmospheric pressure chemical ionization: a case study with ENTACT mixtures
10.1007/s00216-020-02716-3
Introducing the 2016 CASMI contest
10.1016/j.phytol.2017.08.007
Computational Metabolomics (Dagstuhl Seminar 15492)
10.4230/DAGREP.5.11.180
Computational Metabolomics: Identification, Interpretation, Imaging (Dagstuhl Seminar 17491)
10.4230/DAGREP.7.12.1
Performance of combined fragmentation and retention prediction for the identification of organic micropollutants by LC-HRMS
10.1007/s00216-018-0857-5
Ontology-based metabolomics data integration with quality control
10.4155/bio-2018-0303
NORMAN digital sample freezing platform: A European virtual platform to exchange liquid chromatography high resolution-mass spectrometry data and screen suspects in “digitally frozen” environmental samples
10.1016/j.trac.2019.04.008
Let us empower the WFD to prevent risks of chemical pollution in European rivers and lakes
10.1186/s12302-019-0228-7
Future water quality monitoring: improving the balance between exposure and toxicity assessments of real-world pollutant mixtures
10.1186/s12302-019-0193-1
The role of analytical chemistry in exposure science: Focus on the aquatic environment
10.1016/j.chemosphere.2019.01.118
Strengthen the European collaborative environmental research to meet European policy goals for achieving a sustainable, non-toxic environment
10.1186/s12302-019-0232-y
Establish data infrastructure to compile and exchange environmental screening data on a European scale
10.1186/s12302-019-0237-6
High-resolution mass spectrometry to complement monitoring and track emerging chemicals and pollution trends in European water resources
10.1186/s12302-019-0230-0
Computational Metabolomics: From Cheminformatics to Machine Learning (Dagstuhl Seminar 20051)
10.4230/DagRep.10.1.144
Application of preparative capillary gas chromatography (pcGC), automated structure generation and mutagenicity prediction to improve effect-directed analysis of genotoxicants in a contaminated groundwater
10.1007/s11356-009-0286-2
Automated Strategies To Identify Compounds on the Basis of GC/EI-MS and Calculated Properties
10.1021/ac102574h
Automatic recalibration and processing of tandem mass spectra using formula annotation
10.1002/jms.3131
Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation, and Calculated Properties
10.1021/ac203471y
How to confirm identified toxicants in effect-directed analysis
10.1007/s00216-007-1808-8
Identification of a phytotoxic photo-transformation product of diclofenac using effect-directed analysis
10.1016/j.envpol.2009.12.032
Integrated analytical and computer tools for structure elucidation in effect-directed analysis
10.1016/j.trac.2009.03.001
Matching Structures to Mass Spectra Using Fragmentation Patterns: Are the Results As Good As They Look?
10.1021/ac802715e
Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag
10.1186/s13321-021-00489-0
Retrospective non-target analysis to support regulatory water monitoring: from masses of interest to recommendations via in silico workflows
10.1186/s12302-021-00475-1
Discovering Pesticides and their Transformation Products in Luxembourg Waters using Open Cheminformatics Approaches
10.21203/rs.3.rs-478324/v1
FAIR chemical structures in the Journal of Cheminformatics
10.1186/s13321-021-00520-4
Occurrence and Distribution of Pharmaceuticals and Their Transformation Products in Luxembourgish Surface Waters
10.1021/acsenvironau.1c00008
Development and Application of Liquid Chromatographic Retention Time Indices in HRMS-Based Suspect and Nontarget Screening
10.1021/acs.analchem.1c02348
Rene Meier
Meier Rene
ORCID: 0000-0002-1501-1349
A Deep Hydrophobic Binding Cavity is the Main Interaction for Different Y2 R Antagonists.
10.1002/cmdc.201600433
On-resin Diels-Alder reaction with inverse electron demand: an efficient ligation method for complex peptides with a varying spacer to optimize cell adhesion.
10.1039/c6ob00314a
The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein-ligand interactions and implicit COSMO solvation.
10.1039/c5cc09499b
A unique serpin P1' glutamate and a conserved β-sheet C arginine are key residues for activity, protease recognition and stability of serpinA12 (vaspin).
10.1042/bj20150643
Unwinding of the C-Terminal Residues of Neuropeptide Y is critical for Y₂ Receptor Binding and Activation.
10.1002/anie.201411688
Proteolytic activation of prochemerin by kallikrein 7 breaks an ionic linkage and results in C-terminal rearrangement.
10.1042/bj20121880
Selective mode of action of guanidine-containing non-peptides at human NPFF receptors.
10.1021/jm300535s
PARADOCKS – a framework for molecular docking.
10.1186/1758-2946-3-s1-p35
ParaDockS: a framework for molecular docking with population-based metaheuristics.
10.1021/ci900467x
Virtual screening and biological characterization of novel histone arginine methyltransferase PRMT1 inhibitors.
10.1002/cmdc.200800301
Thiobarbiturates as sirtuin inhibitors: virtual screening, free-energy calculations, and biological testing.
10.1002/cmdc.200800104
A new approach for flexible protein-ligand docking based on Particle Swarm Optimisation.
10.1186/1752-153x-2-s1-p6
Structure-activity studies on splitomicin derivatives as sirtuin inhibitors and computational prediction of binding mode.
10.1021/jm700972e
Structure-activity studies on suramin analogues as inhibitors of NAD+-dependent histone deacetylases (sirtuins).
10.1002/cmdc.200700003
Generation of a homology model of the human histamine H(3) receptor for ligand docking and pharmacophore-based screening.
10.1007/s10822-007-9127-x
Adenosine mimetics as inhibitors of NAD+-dependent histone deacetylases, from kinase to sirtuin inhibition.
10.1021/jm060118b
SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses.
10.1021/acs.jcim.6b00513
Bioinformatics can boost metabolomics research.
10.1016/j.jbiotec.2017.05.018
Influence of the hinge region and its adjacent domains on binding and signaling patterns of the thyrotropin and follitropin receptor.
10.1371/journal.pone.0111570
Engineered bacterial polyester hydrolases efficiently degrade polyethylene terephthalate due to relieved product inhibition
10.1002/bit.25941
Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
10.1101/2020.05.09.086066
Wout Bittremieux
Bittremieux Wout
ORCID: 0000-0002-3105-1359
Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania
10.1101/2021.09.14.460245
A learned embedding for efficient joint analysis of millions of mass spectra
10.1101/483263
jqcML: An Open-Source Java API for Mass Spectrometry Quality Control Data in the qcML Format
10.1021/pr401274z
A Primer to Frequent Itemset Mining for Bioinformatics
10.1093/bib/bbt074
qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments
10.1074/mcp.M113.035907
Machine Learning Applications in Proteomics Research: How the Past Can Boost the Future
10.1002/pmic.201300289
Efficient Reduction of Candidate Matches in Peptide Spectrum Library Searching Using the Top k Most Intense Peaks
10.1021/pr401269z
iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring
10.1021/acs.jproteome.5b00127
Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics
10.1021/acs.jproteome.6b00028
On the Feasibility of Mining CD8+ T-Cell Receptor Patterns Underlying Immunogenic Peptide Recognition
10.1007/s00251-017-1023-5
Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph
10.1109/TCBB.2016.2576440
Computational Quality Control Tools for Mass Spectrometry Proteomics
10.1002/pmic.201600159
Designing Biomedical Proteomics Experiments: State-of-the-Art and Future Perspectives
10.1586/14789450.2016.1172967
Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing
10.1021/acs.jproteome.8b00359
The Human Proteome Organization–Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry
10.1021/acs.analchem.6b04310
TCRex: A Webtool for the Prediction of T-Cell Receptor Sequence Epitope Specificity
10.1101/373472
Quality Control in Mass Spectrometry-Based Proteomics
10.1002/mas.21544
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work
10.1021/acs.jproteome.7b00370
Grasping Frequent Subgraph Mining for Bioinformatics Applications
10.1186/s13040-018-0181-9
A Community Proposal to Integrate Proteomics Activities in ELIXIR [Version 1; Referees: 2 Approved]
10.12688/f1000research.11751.1
Proceedings of the EuBIC Developer's Meeting 2018
10.1016/j.jprot.2018.05.015
MESSAR: Automated Recommendation of Metabolite Substructures from Tandem Mass Spectra
10.1101/134189
Extremely fast and accurate open modification spectral library searching of high-resolution mass spectra using feature hashing and graphics processing units
10.1101/627497
Using Expert Driven Machine Learning to Enhance Dynamic Metabolomics Data Analysis
10.3390/metabo9030054
2018 YPIC Challenge: A case study in characterizing an unknown protein sample
10.7287/peerj.preprints.27802v1
2018 YPIC Challenge: A case study in characterizing an unknown protein sample
10.7287/peerj.preprints.27802
On the feasibility of mining CD8+ T-cell receptor patterns underlying immunogenic peptide recognition
10.1101/118539
Fast open modification spectral library searching through approximate nearest neighbor indexing
10.1101/326173
spectrum_utils: A Python package for mass spectrometry data processing and visualization
10.1101/725036
2018 YPIC Challenge: A case study in characterizing an unknown protein sample
10.7287/peerj.preprints.27802v2
Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units
10.1021/acs.jproteome.9b00291
2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample
10.1021/acs.jproteome.9b00384
spectrum_utils: A Python Package for Mass Spectrometry Data Processing and Visualization
10.1021/acs.analchem.9b04884
MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra
10.1371/journal.pone.0226770
Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
10.1101/2020.05.09.086066
Reference data based insights expand understanding of human metabolomes
10.1101/2020.07.08.194159
Current challenges for epitope-agnostic TCR interaction prediction and a new perspective derived from image classification
10.1101/2019.12.18.880146
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data
10.1038/s41587-020-0700-3
Large-scale tandem mass spectrum clustering using fast nearest neighbor searching
10.1101/2021.02.05.429957
Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2
10.1021/acs.jproteome.0c00929
Sharing biological data: why, when, and how
10.1002/1873-3468.14067
The European Bioinformatics Community for Mass Spectrometry (EuBIC‐MS): an open community for bioinformatics training and research
10.1002/rcm.9087
ppx: Programmatic access to proteomics data repositories
10.1101/2021.05.29.446304
Large‐scale tandem mass spectrum clustering using fast nearest neighbor searching
10.1002/rcm.9153
Reference data-set driven metabolomics
10.21203/rs.3.rs-654519/v1
ppx: Programmatic Access to Proteomics Data Repositories
10.1021/acs.jproteome.1c00454
Physicochemical and Pharmacokinetic Properties Determining Drug Detection in Skin
10.1101/2021.08.17.456720
Native Metabolomics Identifies the Rivulariapeptolide Family of Protease Inhibitors
10.1101/2021.09.03.458897
Simon Rogers
Rogers Simon
ORCID: 0000-0003-3578-4477
An Optimal Frequency in Ca2+ Oscillations for Stomatal Closure Is an Emergent Property of Ion Transport in Guard Cells
10.1104/pp.15.01607
Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets.
10.1093/bioinformatics/btv072
MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach.
10.1093/bioinformatics/btu370
Probabilistic assignment of formulas to mass peaks in metabolomics experiments.
10.1093/bioinformatics/btn642
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models.
10.1093/bioinformatics/btn553
Bayesian model-based inference of transcription factor activity.
10.1186/1471-2105-8-S2-S2
Identification of prognostic signatures in breast cancer microarray data using Bayesian techniques.
10.1098/rsif.2005.0093
A Bayesian regression approach to the inference of regulatory networks from gene expression data.
10.1093/bioinformatics/bti487
The latent process decomposition of cDNA microarray data sets.
10.1109/TCBB.2005.29
HDP-Align: Hierarchical Dirichlet Process Clustering for Multiple Peak Alignment of Liquid Chromatography Mass Spectrometry Data
10.1101/074831
Topic modeling for untargeted substructure exploration in metabolomics
10.1073/pnas.1608041113
Global Sensitivity Analysis of OnGuard Models Identifies Key Hubs for Transport Interaction in Stomatal Dynamics
10.1104/pp.17.00170
Unexpected Connections between Humidity and Ion Transport Discovered Using a Model to Bridge Guard Cell-to-Leaf Scales
10.1105/tpc.17.00694
Minimally-destructive atmospheric ionisation mass spectrometry authenticates authorship of historical manuscripts
10.1038/s41598-018-28810-2
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
10.1101/491506
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
EZ-Root-VIS: A Software Pipeline for the Rapid Analysis and Visual Reconstruction of Root System Architecture
10.1104/pp.18.00217
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
10.3390/metabo9070144
In-silico Optimisation of Mass Spectrometry Fragmentation Strategies in Metabolomics
10.1101/744227
In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics
10.3390/metabo9100219
Gestational-age-dependent development of the neonatal metabolome
10.1101/2020.03.27.20045534
Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
10.1101/2020.05.09.086066
Predicting host taxonomic information from viral genomes: A comparison of feature representations
10.1371/journal.pcbi.1007894
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
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
Probabilistic Framework for Integration of Mass Spectrum and Retention Time Information in Small Molecule Identification
10.1101/2020.08.19.255653
matchms - processing and similarity evaluation of mass spectrometry data.
10.21105/joss.02411
Rapid Development of Improved Data-dependent Acquisition Strategies
10.1101/2020.09.11.293092
User guide to the red blood cell model (RCM), a multiplatform JAVA-based model of human red blood cell homeostasis
10.1101/2020.03.07.981779
Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification
10.1093/bioinformatics/btaa998
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
Up-down biphasic volume response of human red blood cells to PIEZO1 activation during capillary transits
10.1371/journal.pcbi.1008706
PIEZO1 and the mechanism of the long circulatory longevity of human red blood cells
10.1371/journal.pcbi.1008496
Rapid Development of Improved Data-Dependent Acquisition Strategies
10.1021/acs.analchem.0c03895
Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches
10.1039/D1NP00023C
Using topic modeling to detect cellular crosstalk in scRNA-seq
10.1101/2021.07.26.453767
Tobias Schulze
Schulze Tobias
ORCID: 0000-0002-9744-8914
Email: tobias.schulze@ufz.de
Estrogen receptor mediated activity in bankside groundwater, with flood suspended particulate matter and floodplain soil - An approach combining tracer substance, bioassay and target analysis
10.1016/j.chemosphere.2011.05.060
Investigation on soil contamination at recently inundated and non-inundated sites
10.1007/s11368-010-0267-6
Identification of a phytotoxic photo-transformation product of diclofenac using effect-directed analysis
10.1016/j.envpol.2009.12.032
Impact of contaminants bound to suspended particulate matter in the context of flood events
10.1007/s11368-010-0262-y
Bioavailability in effect-directed analysis of organic toxicants in sediments
10.1016/j.trac.2009.02.010
Effect-directed analysis of contaminated sediment from the wastewater canal in Pancevo industrial area, Serbia
10.1016/j.chemosphere.2009.08.042
Accelerated membrane-assisted clean-up as a tool for the clean-up of extracts from biological tissues
10.1016/j.chroma.2008.04.071
How to confirm identified toxicants in effect-directed analysis
10.1007/s00216-007-1808-8
The risk of altering soil and sediment samples upon extract preparation for analytical and bio-analytical investigations-a review
10.1007/s00216-008-1933-z
Assessing contamination levels of Laguna Lake sediments (Philippines) using a contact assay with zebrafish (Danio rerio) embryos
10.1016/j.scitotenv.2004.12.002
Identification of novel micropollutants in wastewater by a combination of suspect and nontarget screening
10.1016/j.envpol.2013.07.048
Comparison of different exhaustive and biomimetic extraction techniques for chemical and biological analysis of polycyclic aromatic compounds in river sediments
10.1007/s11368-012-0574-1
Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation, and Calculated Properties
10.1021/ac203471y
Endocrine disrupting, mutagenic, and teratogenic effects of upper Danube River sediments using effect-directed analysis
10.1002/etc.1777
Identification and quantitative confirmation of dinitropyrenes and 3-nitrobenzanthrone as major mutagens in contaminated sediments
10.1016/j.envint.2012.01.010
The German Environmental Specimen Bank: Sampling, processing, and archiving sediment and suspended particulate matter
10.1065/jss2007.08.248
Decoding and Discrimination of Chemical Cues and Signals: Avoidance of Predation and Competition during Parental Care Behavior in Sympatric Poison Frogs
10.1371/journal.pone.0129929
Evaluation of the hazard potentials of river suspended particulate matter and floodplain soils in the Rhine basin using chemical analysis and in vitro bioassays.
10.1007/s11356-014-3707-9
Non-target screening with high-resolution mass spectrometry: critical review using a collaborative trial on water analysis
10.1007/s00216-015-8681-7
Identification of toxicants in sediments: Approaches for integration of effects and bioavailability,Identifizierung toxischer Verbindungen in Sedimenten: Ansätze zur Integration von Wirkung und Bioverfügbarkeit
10.1007/s12302-009-0057-1
Assessing sediments and fish health using a weight-of-evidence approach - In search for the causes of fish decline in the Danube River,Eine Weight-of-Evidence-Studie zur Bewertung der Sedimentbelastung und des Fischrückgangs in der Oberen Donau
10.1007/s12302-009-0063-3
Editorial: Über die Notwendigkeit der wirkungsorientierten Analytik in einer umfassenden Wasserforschung,Editorial: Über die Notwendigkeit der wirkungsorientierten Analytik in einer umfassenden Wasserforschung
10.1007/s12302-009-0068-y
Microbial reporter gene assay as a diagnostic and early warning tool for the detection and characterization of toxic pollution in surface waters
10.1002/etc.3083
EDA-EMERGE: An FP7 initial training network to equip the next generation of young scientists with the skills to address the complexity of environmental contamination with emerging pollutants
10.1186/2190-4715-25-18
Tox-Box: Securing drops of life - An enhanced health-related approach for risk assessment of drinking water in Germany Risk Management of Emerging Compounds and Pathogens in the Water Cycle (RiSKWa)
10.1186/2190-4715-25-27
Identification and evaluation of cyp1a transcript expression in fish as molecular biomarker for petroleum contamination in tropical fresh water ecosystems
10.1016/j.aquatox.2011.02.004
Use of factorial design for the multivariate optimization of polypropylene membranes for the cleanup of environmental samples using the accelerated membrane-assisted cleanup approach
10.1016/j.chroma.2011.12.069
Effect-directed analysis supporting monitoring of aquatic environments - An in-depth overview
10.1016/j.scitotenv.2015.11.102
Linking in Vitro Effects and Detected Organic Micropollutants in Surface Water Using Mixture-Toxicity Modeling
10.1021/acs.est.5b04083
DDT and metabolites in aquatic sediments of Berlin area: Occurrence, analysis and ecotoxical potential,DDT und metaboliten in sedimenten Berliner gewässer: Vorkommen, analytik und schädigungspotenzial
10.1065/uwsf2002.05.026
Ecotoxicological assessment of sediments and suspended particulate matter - Potential risk of ground-water contamination and correlation of different exposure routes (organic extract, whole sediment) in the bacterial contact assay and the fish egg assay,Ökotoxikologische untersuchung von sedimenten und schwebstoffen: Abschätzung des gefährdungspotenzials für trinkwasser und korrelation verschiedener expositionspfade (acetonischer extrakt, natives sediment) im bakterienkontakttest und fischeitest
10.1065/uwsf2002.07.036
Micropollutants in European rivers: A mode of action survey to support the development of effect-based tools for water monitoring
10.1002/etc.3460
Impact of untreated wastewater on a major European river evaluated with a combination of in vitro bioassays and chemical analysis
10.1016/j.envpol.2016.11.011
European demonstration program on the effect-based and chemical identification and monitoring of organic pollutants in European surface waters
10.1016/j.scitotenv.2017.06.032
Solid-phase extraction as sample preparation of water samples for cell-based and other in vitro bioassays
10.1039/C7EM00555E
NORMAN digital sample freezing platform: A European virtual platform to exchange liquid chromatography high resolution-mass spectrometry data and screen suspects in “digitally frozen” environmental samples
10.1016/j.trac.2019.04.008
The metaRbolomics Toolbox in Bioconductor and beyond
10.3390/metabo9100200
Estrogenic activity of surface waters using zebrafish- and human-based in vitro assays: The Danube as a case-study
10.1016/j.etap.2020.103401
Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
10.1101/2020.05.09.086066
Application of the Sea Urchin Embryo Test in Toxicity Evaluation and Effect-Directed Analysis of Wastewater Treatment Plant Effluents
10.1021/acs.est.0c01504
Symbolic Aggregate Approximation Improves Gap Filling in High-Resolution Mass Spectrometry Data Processing
10.1021/acs.analchem.0c00899
Correction to Symbolic Aggregate Approximation Improves Gap Filling in High-Resolution Mass Spectrometry Data Processing
10.1021/acs.analchem.1c00530
Sampling and Conservation
10.1016/B978-0-444-53199-5.00054-3
Assessing the Mixture Effects in in Vitro Bioassays of Chemicals Occurring in Small Agricultural Streams during Rain Events
10.1021/acs.est.0c02235
Effect-based assessment of toxicity removal during wastewater treatment
10.1016/j.watres.2017.09.014
Unraveling longitudinal pollution patterns of organic micropollutants in a river by non-target screening and cluster analysis
10.1016/j.scitotenv.2020.138388
Corrigendum to “European demonstration program on the effect-based and chemical identification and monitoring of organic pollutants in European surface waters” [Sci. Total Environ. 601–602 (2017) 1849–1868] (S0048969717314365) (10.1016/j.scitotenv.2017.06.032))
10.1016/j.scitotenv.2018.04.356
Screening of Pesticide and Biocide Patterns As Risk Drivers in Sediments of Major European River Mouths: Ubiquitous or River Basin-Specific Contamination?
10.1021/acs.est.7b04355
A sediment extraction and cleanup method for wide-scope multitarget screening by liquid chromatography–high-resolution mass spectrometry
10.1007/s00216-017-0708-9
A European proposal for quality control and quality assurance of tandem mass spectral libraries
10.1186/s12302-020-00314-9
SPLASH, a hashed identifier for mass spectra
10.1038/nbt.3689
The NORMAN Association and the European Partnership for Chemicals Risk Assessment (PARC): let’s cooperate!
10.1186/s12302-020-00375-w
Future water quality monitoring: improving the balance between exposure and toxicity assessments of real-world pollutant mixtures
10.1186/s12302-019-0193-1
Prioritising site-specific micropollutants in surface water from LC-HRMS non-target screening data using a rarity score
10.1186/s12302-019-0231-z
Establish data infrastructure to compile and exchange environmental screening data on a European scale
10.1186/s12302-019-0237-6
High-resolution mass spectrometry to complement monitoring and track emerging chemicals and pollution trends in European water resources
10.1186/s12302-019-0230-0
Mutagenicity in Surface Waters: Synergistic Effects of Carboline Alkaloids and Aromatic Amines
10.1021/acs.est.6b05468
Optimization of LC-Orbitrap-HRMS acquisition and MZmine 2 data processing for nontarget screening of environmental samples using design of experiments
10.1007/s00216-016-9919-8
Performance of combined fragmentation and retention prediction for the identification of organic micropollutants by LC-HRMS
10.1007/s00216-018-0857-5
The impact of chemosensitisation on bioaccumulation and sediment toxicity
10.1016/j.chemosphere.2017.08.019
Characterization and risk assessment of seasonal and weather dynamics in organic pollutant mixtures from discharge of a separate sewer system
10.1016/j.watres.2018.02.002
Bioassay battery interlaboratory investigation of emerging contaminants in spiked water extracts – Towards the implementation of bioanalytical monitoring tools in water quality assessment and monitoring
10.1016/j.watres.2016.08.018
A data set of 255,000 randomly selected and manually classified extracted ion chromatograms for evaluation of peak detection methods
10.3390/metabo10040162
Measuring the internal concentration of volatile organic compounds in small organisms using micro-QuEChERS coupled to LVI–GC–MS/MS
10.1007/s00216-017-0532-2
Towards a holistic and solution-oriented monitoring of chemical status of European water bodies: how to support the EU strategy for a non-toxic environment?
10.1186/s12302-018-0161-1
Looking back - Looking forward: A novel multi-time slice weight-of-evidence approach for defining reference conditions to assess the impact of human activities on lake systems
10.1016/j.scitotenv.2018.01.113
Assessment of a novel device for onsite integrative large-volume solid phase extraction of water samples to enable a comprehensive chemical and effect-based analysis
10.1016/j.scitotenv.2016.12.140
Evidence for antifouling biocides as one of the limiting factors for the recovery of macrophyte communities in lakes of Schleswig-Holstein
10.1186/s12302-021-00500-3
Improving the Screening Analysis of Pesticide Metabolites in Human Biomonitoring by Combining High-Throughput In Vitro Incubation and Automated LC–HRMS Data Processing
10.1021/acs.analchem.1c00972
Sources and Fate of the Antiandrogenic Fluorescent Dye 4‐Methyl‐7‐Diethylaminocoumarin in Small River Systems
10.1002/etc.5181
Development and Application of Liquid Chromatographic Retention Time Indices in HRMS-Based Suspect and Nontarget Screening
10.1021/acs.analchem.1c02348
