Mining molecular structure databases: Identification of small molecules based on fragmentation mass spectrometry data

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

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

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

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics

(2015) Arpana Vaniya et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

In Silico Prediction and Automatic LC–MSn Annotation of Green Tea Metabolites in Urine

(2014) Lars Ridder et al.   ANALYTICAL CHEMISTRY

MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics

(2014) Yingfeng Wang et al.   ANALYTICAL CHEMISTRY

Bioinformatics: The Next Frontier of Metabolomics

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

Metabolite identification through multiple kernel learning on fragmentation trees

(2014) Huibin Shen et al.   BIOINFORMATICS

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

(2014) Felicity Allen et al.   Metabolomics

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

(2014) Franziska Hufsky et al.   NATURAL PRODUCT REPORTS

A community computational challenge to predict the activity of pairs of compounds

(2014) Mukesh Bansal et al.   NATURE BIOTECHNOLOGY

A community effort to assess and improve drug sensitivity prediction algorithms

(2014) James C Costello et al.   NATURE BIOTECHNOLOGY

XTMS: pathway design in an eXTended metabolic space

(2014) Pablo Carbonell et al.   NUCLEIC ACIDS RESEARCH

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra

(2014) Felicity Allen et al.   NUCLEIC ACIDS RESEARCH

Systematic Structural Characterization of Metabolites inArabidopsisvia Candidate Substrate-Product Pair Networks

(2014) Kris Morreel et al.   PLANT CELL

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

Automated Pipeline for De Novo Metabolite Identification Using Mass-Spectrometry-Based Metabolomics

(2013) Julio E. Peironcely et al.   ANALYTICAL CHEMISTRY

MyCompoundID: Using an Evidence-Based Metabolome Library for Metabolite Identification

(2013) Liang Li et al.   ANALYTICAL CHEMISTRY

Automatic Chemical Structure Annotation of an LC–MSn Based Metabolic Profile from Green Tea

(2013) Lars Ridder et al.   ANALYTICAL CHEMISTRY

In Silico Enzymatic Synthesis of a 400 000 Compound Biochemical Database for Nontargeted Metabolomics

(2013) Lochana C. Menikarachchi et al.   Journal of Chemical Information and Modeling

Finding Maximum Colorful Subtrees in Practice

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

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

MS/MS networking guided analysis of molecule and gene cluster families

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

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP) - round x

(2013) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational mass spectrometry for small-molecule fragmentation

(2013) Franziska Hufsky et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

De novo analysis of electron impact mass spectra using fragmentation trees

(2012) Franziska Hufsky et al.   ANALYTICA CHIMICA ACTA

Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation, and Calculated Properties

(2012) Emma L. Schymanski et al.   ANALYTICAL CHEMISTRY

MolFind: A Software Package Enabling HPLC/MS-Based Identification of Unknown Chemical Structures

(2012) Lochana C. Menikarachchi et al.   ANALYTICAL CHEMISTRY

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

(2012) Stephen Stein   ANALYTICAL CHEMISTRY

Structural Elucidation and Quantification of Phenolic Conjugates Present in Human Urine after Tea Intake

(2012) Justin J. J. van der Hooft et al.   ANALYTICAL CHEMISTRY

Metabolite Identification Using Automated Comparison of High-Resolution Multistage Mass Spectral Trees

(2012) Miquel Rojas-Cherto et al.   ANALYTICAL CHEMISTRY

Metabolite identification and molecular fingerprint prediction through machine learning

(2012) M. Heinonen et al.   BIOINFORMATICS

In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids

(2012) Lars J. Kangas et al.   BIOINFORMATICS

Structural Annotation and Elucidation of Conjugated Phenolic Compounds in Black, Green, and White Tea Extracts

(2012) Justin J. J. van der Hooft et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature

(2012) Paul G. Arnison et al.   NATURAL PRODUCT REPORTS

Metabolomics: the apogee of the omics trilogy

(2012) Gary J. Patti et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

HMDB 3.0—The Human Metabolome Database in 2013

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

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

Substructure-based annotation of high-resolution multistage MSnspectral trees

(2012) Lars Ridder et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Metabolomics: from small molecules to big ideas

(2011) Monya Baker   NATURE METHODS

Computing Fragmentation Trees from Tandem Mass Spectrometry Data

(2010) Florian Rasche et al.   ANALYTICAL CHEMISTRY

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

Determination of ion structures in structurally related compounds using precursor ion fingerprinting

(2008) Michelle T. Sheldon et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

FiD: a software forab initiostructural identification of product ions from tandem mass spectrometric data

(2008) Markus Heinonen et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

In Silico Tools for Sharing Data and Knowledge on Toxicity and Metabolism: Derek for Windows, Meteor, and Vitic

(2008) Carol A. Marchant et al.   TOXICOLOGY MECHANISMS AND METHODS