Feature-based molecular networking in the GNPS analysis environment

Mass spectrometry searches using MASST

(2020) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

AutoTuner: High Fidelity and Robust Parameter Selection for Metabolomics Data Processing

(2020) Craig McLean et al.   ANALYTICAL CHEMISTRY

A lipidome atlas in MS-DIAL 4

(2020) Hiroshi Tsugawa et al.   NATURE BIOTECHNOLOGY

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

(2019) Kai Dührkop et al.   NATURE METHODS

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics

(2019) Nils Hoffmann et al.   ANALYTICAL CHEMISTRY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

(2019) Madeleine Ernst et al.   Metabolites

Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation

(2018) Louis-Félix Nothias et al.   JOURNAL OF NATURAL PRODUCTS

Propagating annotations of molecular networks using in silico fragmentation

(2018) Ricardo R. da Silva et al.   PLoS Computational Biology

Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra

(2018) Alexey Gurevich et al.   Nature Microbiology

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

Metwork: a web server for natural products anticipation

(2018) Yann Beauxis et al.   BIOINFORMATICS

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

(2018) Florian Meier et al.   MOLECULAR & CELLULAR PROTEOMICS

Commensal bacteria make GPCR ligands that mimic human signalling molecules

(2017) Louis J. Cohen et al.   NATURE

3D molecular cartography using LC–MS facilitated by Optimus and 'ili software

(2017) Ivan Protsyuk et al.   Nature Protocols

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

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

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

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

(2016) Hannes L Röst et al.   NATURE METHODS

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

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

IPO: a tool for automated optimization of XCMS parameters

(2015) Gunnar Libiseller et al.   BMC BIOINFORMATICS

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

MetaboAnalyst 3.0—making metabolomics more meaningful

(2015) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist

(2015) Louis J. Cohen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2014) Felicity Allen et al.   Metabolomics

Metabolite Profiling of a NIST Standard Reference Material for Human Plasma (SRM 1950): GC-MS, LC-MS, NMR, and Clinical Laboratory Analyses, Libraries, and Web-Based Resources

(2013) Yamil Simón-Manso et al.   ANALYTICAL CHEMISTRY

Quantitative molecular networking to profile marine cyanobacterial metabolomes

(2013) Jacob R Winnikoff et al.   JOURNAL OF ANTIBIOTICS

MetFusion: integration of compound identification strategies

(2013) Michael Gerlich et al.   JOURNAL OF MASS SPECTROMETRY

LipidBlast in silico tandem mass spectrometry database for lipid identification

(2013) Tobias Kind et al.   NATURE METHODS

TOPPAS: A Graphical Workflow Editor for the Analysis of High-Throughput Proteomics Data

(2012) Johannes Junker et al.   JOURNAL OF PROTEOME RESEARCH

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

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

A massively spectacular view of the chemical lives of microbes

(2012) M. F. Traxler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets

(2011) Carsten Kuhl et al.   ANALYTICAL CHEMISTRY

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

Highly sensitive feature detection for high resolution LC/MS

(2008) Ralf Tautenhahn et al.   BMC BIOINFORMATICS

Clustering Millions of Tandem Mass Spectra

(2007) Ari M. Frank et al.   JOURNAL OF PROTEOME RESEARCH