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

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

Metabolite identification through multiple kernel learning on fragmentation trees

(2014) Huibin Shen et al.   BIOINFORMATICS

The Royal Society of Chemistry and the delivery of chemistry data repositories for the community

(2014) Antony Williams et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2014) Felicity Allen et al.   Metabolomics

Metabolomic data streaming for biology-dependent data acquisition

(2014) Duane Rinehart et al.   NATURE BIOTECHNOLOGY

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

(2014) Kris Morreel et al.   PLANT CELL

Efficient ring perception for the Chemistry Development Kit

(2014) John W May et al.   Journal of Cheminformatics

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

Automated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data

(2013) Erhan Kenar et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Computational mass spectrometry for small-molecule fragmentation

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

Computational mass spectrometry for small molecules

(2013) Kerstin Scheubert et al.   Journal of Cheminformatics

Identifying the Unknowns by Aligning Fragmentation Trees

(2012) Florian Rasche et al.   ANALYTICAL CHEMISTRY

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

(2012) Stephen Stein   ANALYTICAL CHEMISTRY

Fast alignment of fragmentation trees

(2012) Franziska Hufsky et al.   BIOINFORMATICS

Metabolite identification and molecular fingerprint prediction through machine learning

(2012) M. Heinonen et al.   BIOINFORMATICS

Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics

(2012) Warwick B. Dunn et al.   Metabolomics

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

Metabolomics: the apogee of the omics trilogy

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

Database resources of the National Center for Biotechnology Information

(2012)   NUCLEIC ACIDS RESEARCH

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

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

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

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

Metabolomics: from small molecules to big ideas

(2011) Monya Baker   NATURE METHODS

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Computing Fragmentation Trees from Tandem Mass Spectrometry Data

(2010) Florian Rasche et al.   ANALYTICAL CHEMISTRY

In silico fragmentation for computer assisted identification of metabolite mass spectra

(2010) Sebastian Wolf et al.   BMC BIOINFORMATICS

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

Chemical substructures that enrich for biological activity

(2008) Justin Klekota et al.   BIOINFORMATICS

Automated de novo protein sequencing of monoclonal antibodies

(2008) Nuno Bandeira et al.   NATURE BIOTECHNOLOGY

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

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