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

Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints

(2018) Marcus Ludwig et al.   BIOINFORMATICS

Commensal bacteria make GPCR ligands that mimic human signalling molecules

(2017) Louis J. Cohen et al.   NATURE

Critical Assessment of Small Molecule Identification 2016: automated methods

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

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

(2017) Egon L. Willighagen et al.   Journal of Cheminformatics

Predicting the Presence of Uncommon Elements in Unknown Biomolecules from Isotope Patterns

(2016) Marvin Meusel et al.   ANALYTICAL CHEMISTRY

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

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Revealing disease-associated pathways by network integration of untargeted metabolomics

(2016) Leila Pirhaji et al.   NATURE METHODS

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

(2016) Hannes L Röst et al.   NATURE METHODS

Fragmentation trees reloaded

(2016) Sebastian Böcker et al.   Journal of Cheminformatics

Deep learning

(2015) Yann LeCun et al.   NATURE

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

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

PubChem Substance and Compound databases

(2015) Sunghwan Kim 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

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

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

Metabolite identification through multiple kernel learning on fragmentation trees

(2014) Huibin Shen et al.   BIOINFORMATICS

Finding Maximum Colorful Subtrees in Practice

(2013) Imran Rauf et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Highly Accurate Chemical Formula Prediction Tool Utilizing High-Resolution Mass Spectra, MS/MS Fragmentation, Heuristic Rules, and Isotope Pattern Matching

(2012) Tomáš Pluskal et al.   ANALYTICAL CHEMISTRY

Metabolite identification and molecular fingerprint prediction through machine learning

(2012) M. Heinonen et al.   BIOINFORMATICS

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

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

ChemSpider: An Online Chemical Information Resource

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

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

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

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

Towards de novo identification of metabolites by analyzing tandem mass spectra

(2008) S. Bocker et al.   BIOINFORMATICS

SIRIUS: decomposing isotope patterns for metabolite identification†

(2008) Sebastian Böcker et al.   BIOINFORMATICS

Combinatorial Approaches for Mass Spectra Recalibration

(2008) S. Bocker et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics