Global chemical analysis of biology by mass spectrometry

High-efficiency multiphoton boson sampling

(2017) Hui Wang et al.   Nature Photonics

Metabolizing Data in the Cloud

(2017) Benedikt Warth et al.   TRENDS IN BIOTECHNOLOGY

Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy

(2017) Robert A. Quinn et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Critical Assessment of Small Molecule Identification 2016: automated methods

(2017) Emma L. Schymanski et al.   Journal of Cheminformatics

Identifying known unknowns using the US EPA’s CompTox Chemistry Dashboard

(2016) Andrew D. McEachran et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses

(2016) J. Rafael Montenegro-Burke et al.   ANALYTICAL CHEMISTRY

Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication

(2016) Pierre-Marie Allard et al.   ANALYTICAL CHEMISTRY

Fast metabolite identification with Input Output Kernel Regression

(2016) Céline Brouard et al.   BIOINFORMATICS

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future

(2016) Stephen Barnes et al.   JOURNAL OF MASS SPECTROMETRY

How to Compute Electron Ionization Mass Spectra from First Principles

(2016) Christoph Alexander Bauer et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

(2016) Fanni Laura Bazsó et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Non-targeted UHPLC-MS metabolomic data processing methods: a comparative investigation of normalisation, missing value imputation, transformation and scaling

(2016) Riccardo Di Guida et al.   Metabolomics

The evolution of genome mining in microbes – a review

(2016) Nadine Ziemert et al.   NATURAL PRODUCT REPORTS

Technology: Smartphone science

(2016) Jon Cartwright   NATURE

Microbiome-wide association studies link dynamic microbial consortia to disease

(2016) Jack A. Gilbert et al.   NATURE

1,500 scientists lift the lid on reproducibility

(2016) Monya Baker   NATURE

SPLASH, a hashed identifier for mass spectra

(2016) Gert Wohlgemuth et al.   NATURE BIOTECHNOLOGY

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Dereplication of peptidic natural products through database search of mass spectra

(2016) Hosein Mohimani et al.   Nature Chemical Biology

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

(2016) Jianwei Sun et al.   Nature Chemistry

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

The past, present and future of microbiome analyses

(2016) Richard Allen White et al.   Nature Protocols

Illuminating a plant’s tissue-specific metabolic diversity using computational metabolomics and information theory

(2016) Dapeng Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topic modeling for untargeted substructure exploration in metabolomics

(2016) Justin Johan Jozias van der Hooft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep sequencing of 10,000 human genomes

(2016) Amalio Telenti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mass spectral databases for LC/MS- and GC/MS-based metabolomics: State of the field and future prospects

(2016) Maria Vinaixa et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Direct evidence of the molecular basis for biological silicon transport

(2016) Michael J. Knight et al.   Nature Communications

The WEIZMASS spectral library for high-confidence metabolite identification

(2016) Nir Shahaf et al.   Nature Communications

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

(2016) Yannick Djoumbou Feunang et al.   Journal of Cheminformatics

MetFrag relaunched: incorporating strategies beyond in silico fragmentation

(2016) Christoph Ruttkies et al.   Journal of Cheminformatics

Metabolic profile and safety of piperlongumine

(2016) Fernanda de Lima Moreira et al.   Scientific Reports

Wearable Chemical Sensors: Present Challenges and Future Prospects

(2016) Amay J. Bandodkar et al.   ACS Sensors

Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease

(2016) Qiang Feng et al.   Scientific Reports

MyCompoundID MS/MS Search: Metabolite Identification Using a Library of Predicted Fragment-Ion-Spectra of 383,830 Possible Human Metabolites

(2015) Tao Huan et al.   ANALYTICAL CHEMISTRY

Innovation in metabolomics to improve personalized healthcare

(2015) Stefano Cacciatore et al.   Annals of the New York Academy of Sciences

MetaMapR: pathway independent metabolomic network analysis incorporating unknowns: Fig. 1.

(2015) Dmitry Grapov et al.   BIOINFORMATICS

Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction

(2015) A Ranjitha Dhanasekaran et al.   BMC BIOINFORMATICS

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

(2015) Katherine R. Duncan et al.   CHEMISTRY & BIOLOGY

Effective Use of Mass Spectrometry in the Clinical Laboratory

(2015) P. J. Jannetto et al.   CLINICAL CHEMISTRY

Missing value imputation strategies for metabolomics data

(2015) Emily Grace Armitage et al.   ELECTROPHORESIS

Updates in metabolomics tools and resources: 2014-2015

(2015) Biswapriya B. Misra et al.   ELECTROPHORESIS

Complexity of Naturally Produced Polybrominated Diphenyl Ethers Revealed via Mass Spectrometry

(2015) Vinayak Agarwal et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

(2015) Reza M. Salek et al.   Metabolomics

Minimum Information about a Biosynthetic Gene cluster

(2015) Marnix H Medema et al.   Nature Chemical Biology

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

(2015) Manish Sud et al.   NUCLEIC ACIDS RESEARCH

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

(2015) Kai Dührkop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Illuminating the dark matter in metabolomics: Fig. 1.

(2015) Ricardo R. da Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular cartography of the human skin surface in 3D

(2015) Amina Bouslimani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products

(2015) Chad W. Johnston et al.   Nature Communications

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

(2015) James G Jeffryes et al.   Journal of Cheminformatics

Local false discovery rate estimation using feature reliability in LC/MS metabolomics data

(2015) Elizabeth Y. Chong et al.   Scientific Reports

Automated Genome Mining of Ribosomal Peptide Natural Products

(2014) Hosein Mohimani et al.   ACS Chemical Biology

Bioinformatics: The Next Frontier of Metabolomics

(2014) Caroline H. Johnson et al.   ANALYTICAL CHEMISTRY

Mass Spectrometry, Review of the Basics: Ionization

(2014) Hanan Awad et al.   APPLIED SPECTROSCOPY REVIEWS

NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery

(2014) Hosein Mohimani et al.   JOURNAL OF NATURAL PRODUCTS

Metabolite identification: are you sure? And how do your peers gauge your confidence?

(2014) Darren J. Creek et al.   Metabolomics

Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification

(2014) Felicity Allen et al.   Metabolomics

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience

(2014) Johannes Griss et al.   MOLECULAR & CELLULAR PROTEOMICS

New kids on the block: novel informatics methods for natural product discovery

(2014) Franziska Hufsky et al.   NATURAL PRODUCT REPORTS

Metabolomic data streaming for biology-dependent data acquisition

(2014) Duane Rinehart et al.   NATURE BIOTECHNOLOGY

Biosynthesis of polybrominated aromatic organic compounds by marine bacteria

(2014) Vinayak Agarwal et al.   Nature Chemical Biology

T3DB: the toxic exposome database

(2014) David Wishart et al.   NUCLEIC ACIDS RESEARCH

Quest for a universal density functional: the accuracy of density functionals across a broad spectrum of databases in chemistry and physics

(2014) R. Peverati et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

The Skin Microbiome in Healthy and Allergic Dogs

(2014) Aline Rodrigues Hoffmann et al.   PLoS One

Wireless gas detection with a smartphone via rf communication

(2014) Joseph M. Azzarelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS

(2014) Q. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LIFE SCIENCE TECHNOLOGIES: Miniaturizing Mass Spectrometry

(2014) J. M. Perkel   SCIENCE

Impact of Endophytic Microorganisms on Plants, Environment and Humans

(2014) Dhanya N. Nair et al.   TheScientificWorldJOURNAL

Standardized description of scientific evidence using the Evidence Ontology (ECO)

(2014) M. C. Chibucos et al.   Database-The Journal of Biological Databases and Curation

Meta-analyses of studies of the human microbiota

(2013) C. A. Lozupone et al.   GENOME RESEARCH

Databases of the thiotemplate modular systems (CSDB) and their in silico recombinants (r-CSDB)

(2013) Janko Diminic et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

High-Resolution MS, MS/MS, and UV Database of Fungal Secondary Metabolites as a Dereplication Protocol for Bioactive Natural Products

(2013) Tamam El-Elimat et al.   JOURNAL OF NATURAL PRODUCTS

LipidBlast in silico tandem mass spectrometry database for lipid identification

(2013) Tobias Kind et al.   NATURE METHODS

Evaluation of Normalization Methods to Pave the Way Towards Large-Scale LC-MS-Based Metabolomics Profiling Experiments

(2013) Bedilu Alamirie Ejigu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

AfroDb: A Select Highly Potent and Diverse Natural Product Library from African Medicinal Plants

(2013) Fidele Ntie-Kang et al.   PLoS One

Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules

(2013) R. D. Kersten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In vitrometabolism of monensin A: microbial and human liver microsomes models

(2013) Bruno A. Rocha et al.   XENOBIOTICA

InChI - the worldwide chemical structure identifier standard

(2013) Stephen Heller et al.   Journal of Cheminformatics

Cohabiting family members share microbiota with one another and with their dogs

(2013) Se Jin Song et al.   eLife

Mass Spectral Reference Libraries: An Ever-Expanding Resource for Chemical Identification

(2012) Stephen Stein   ANALYTICAL CHEMISTRY

XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data

(2012) Ralf Tautenhahn et al.   ANALYTICAL CHEMISTRY

Tools for the functional interpretation of metabolomic experiments

(2012) M. Chagoyen et al.   BRIEFINGS IN BIOINFORMATICS

File Formats Commonly Used in Mass Spectrometry Proteomics

(2012) Eric W. Deutsch   MOLECULAR & CELLULAR PROTEOMICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

An accelerated workflow for untargeted metabolomics using the METLIN database

(2012) Ralf Tautenhahn et al.   NATURE BIOTECHNOLOGY

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

(2012) Kenneth Haug et al.   NUCLEIC ACIDS RESEARCH

HMDB 3.0—The Human Metabolome Database in 2013

(2012) David S. Wishart et al.   NUCLEIC ACIDS RESEARCH

RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database

(2012) Yuji Sawada et al.   PHYTOCHEMISTRY

Mass spectral molecular networking of living microbial colonies

(2012) J. Watrous et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery

(2012) A. Ibrahim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The importance of experimental design and QC samples in large-scale and MS-driven untargeted metabolomic studies of humans

(2012) Warwick B Dunn et al.   Bioanalysis

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Quality evaluation of tandem mass spectral libraries

(2011) Herbert Oberacher et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

The volatile compound BinBase mass spectral database

(2011) Kirsten Skogerson et al.   BMC BIOINFORMATICS

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

(2011) Hélène Ferry-Dumazet et al.   BMC PLANT BIOLOGY

Gene set enrichment analysis: performance evaluation and usage guidelines

(2011) J.-H. Hung et al.   BRIEFINGS IN BIOINFORMATICS

Targeted and Non-Targeted Boron Complex Formation followed by Electrospray Fourier Transform Ion Cyclotron Mass Spectrometry: A Novel Approach for Identifying Boron Esters with Natural Organic Matter

(2011) Andras Gaspar et al.   EUROPEAN JOURNAL OF MASS SPECTROMETRY

Initial Experimental Characterization of a New Ultra-High Resolution FTICR Cell with Dynamic Harmonization

(2011) Eugene N. Nikolaev et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Targeted Mass Spectrometric Approach for Biomarker Discovery and Validation with Nonglycosylated Tryptic Peptides from N-linked Glycoproteins in Human Plasma

(2011) Ju Yeon Lee et al.   MOLECULAR & CELLULAR PROTEOMICS

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

A mass spectrometry–guided genome mining approach for natural product peptidogenomics

(2011) Roland D Kersten et al.   Nature Chemical Biology

Databases aim to bridge the East-West divide of drug discovery

(2011) Katharine Sanderson   NATURE MEDICINE

The Human Serum Metabolome

(2011) Nikolaos Psychogios et al.   PLoS One

High-throughput walkthrough detection portal for counter terrorism: detection of triacetone triperoxide (TATP) vapor by atmospheric-pressure chemical ionization ion trap mass spectrometry

(2011) Yasuaki Takada et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

Detection of lung, breast, colorectal and prostate cancers from exhaled breath using a single array of nanosensors

(2010) G Peng et al.   BRITISH JOURNAL OF CANCER

ChemSpider: An Online Chemical Information Resource

(2010) Harry E. Pence et al.   JOURNAL OF CHEMICAL EDUCATION

MassBank: a public repository for sharing mass spectral data for life sciences

(2010) Hisayuki Horai et al.   JOURNAL OF MASS SPECTROMETRY

Dealing with the unknown: Metabolomics and Metabolite Atlases

(2010) Benjamin P. Bowen et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics

(2009) M. Brown et al.   ANALYST

ESI-MS/MS library of 1,253 compounds for application in forensic and clinical toxicology

(2009) Sebastian Dresen et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Mass Spectrometry, Review of the Basics: Electrospray, MALDI, and Commonly Used Mass Analyzers

(2009) Anas El-Aneed et al.   APPLIED SPECTROSCOPY REVIEWS

Unifying biological image formats with HDF5

(2009) Matthew T. Dougherty et al.   COMMUNICATIONS OF THE ACM

Biohalogenation: Nature’s Way to Synthesize Halogenated Metabolites†

(2009) Claudia Wagner et al.   JOURNAL OF NATURAL PRODUCTS

MetaboAnalyst: a web server for metabolomic data analysis and interpretation

(2009) J. Xia et al.   NUCLEIC ACIDS RESEARCH

SIRIUS: decomposing isotope patterns for metabolite identification†

(2008) Sebastian Böcker et al.   BIOINFORMATICS

SyGMa: Combining Expert Knowledge and Empirical Scoring in the Prediction of Metabolites

(2008) Lars Ridder et al.   ChemMedChem

Mass spectrometry and illicit drug testing: analytical challenges of the anti-doping laboratories

(2008) Francesco Botrè   Expert Review of Proteomics

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

The minimum information about a genome sequence (MIGS) specification

(2008) Dawn Field et al.   NATURE BIOTECHNOLOGY