Published in J Cheminform on March 01, 2013
Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc Natl Acad Sci U S A (2015) 1.10
Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics. Trends Analyt Chem (2015) 0.93
Metabolite identification through multiple kernel learning on fragmentation trees. Bioinformatics (2014) 0.87
Open-access metabolomics databases for natural product research: present capabilities and future potential. Front Bioeng Biotechnol (2015) 0.86
Computational analyses of spectral trees from electrospray multi-stage mass spectrometry to aid metabolite identification. Metabolites (2013) 0.81
Functional genomics of novel secondary metabolites from diverse cyanobacteria using untargeted metabolomics. Mar Drugs (2013) 0.80
Fragmentation trees reloaded. J Cheminform (2016) 0.75
Trends in the application of high-resolution mass spectrometry for human biomonitoring: An analytical primer to studying the environmental chemical space of the human exposome. Environ Int (2017) 0.75
Technical Challenges in Mass Spectrometry-Based Metabolomics. Mass Spectrom (Tokyo) (2016) 0.75
Towards automated discrimination of lipids versus peptides from full scan mass spectra. EuPA Open Proteom (2014) 0.75
Identification and Partial Structural Characterization of Mass Isolated Valsartan and Its Metabolite with Messenger Tagging Vibrational Spectroscopy. J Am Soc Mass Spectrom (2017) 0.75
Elucidating the Structure of N(1)-Acetylisoputreanine: A Novel Polyamine Catabolite in Human Urine. ACS Omega (2017) 0.75
CASMI 2016: A manual approach for dereplication of natural products using tandem mass spectrometry. Phytochem Lett (2017) 0.75
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol (2008) 38.00
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem (2006) 15.00
HMDB: the Human Metabolome Database. Nucleic Acids Res (2007) 13.38
HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res (2008) 11.23
METLIN: a metabolite mass spectral database. Ther Drug Monit (2005) 10.15
Metabolite profiling for plant functional genomics. Nat Biotechnol (2000) 8.74
GMD@CSB.DB: the Golm Metabolome Database. Bioinformatics (2004) 7.33
Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI). Metabolomics (2007) 6.93
Mass spectrometry sampling under ambient conditions with desorption electrospray ionization. Science (2004) 6.68
MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom (2010) 6.16
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics (2010) 5.77
MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics (2006) 5.38
Innovation: Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol (2012) 5.19
Metabolite identification via the Madison Metabolomics Consortium Database. Nat Biotechnol (2008) 5.12
Toward interoperable bioscience data. Nat Genet (2012) 4.72
Potential of metabolomics as a functional genomics tool. Trends Plant Sci (2004) 4.10
FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem (2009) 3.71
Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics (2007) 3.70
Mass spectral molecular networking of living microbial colonies. Proc Natl Acad Sci U S A (2012) 3.56
Optimization and testing of mass spectral library search algorithms for compound identification. J Am Soc Mass Spectrom (1994) 3.46
A proposed framework for the description of plant metabolomics experiments and their results. Nat Biotechnol (2004) 3.32
Metabolite profiling: from diagnostics to systems biology. Nat Rev Mol Cell Biol (2004) 3.31
Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat Biotechnol (2004) 3.30
MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal Chem (2009) 3.30
XCMS Online: a web-based platform to process untargeted metabolomic data. Anal Chem (2012) 3.24
Data processing for mass spectrometry-based metabolomics. J Chromatogr A (2007) 3.21
Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom (1997) 3.03
Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm. BMC Bioinformatics (2006) 3.02
Automated de novo protein sequencing of monoclonal antibodies. Nat Biotechnol (2008) 3.02
TagFinder for the quantitative analysis of gas chromatography--mass spectrometry (GC-MS)-based metabolite profiling experiments. Bioinformatics (2008) 3.01
On the proper use of mass accuracy in proteomics. Mol Cell Proteomics (2006) 2.76
CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal Chem (2011) 2.76
In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics (2010) 2.61
An accelerated workflow for untargeted metabolomics using the METLIN database. Nat Biotechnol (2012) 2.56
The metabolomics standards initiative. Nat Biotechnol (2007) 2.54
Observing and interpreting correlations in metabolomic networks. Bioinformatics (2003) 2.49
Structural diversity of organic chemistry. A scaffold analysis of the CAS Registry. J Org Chem (2008) 2.45
Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol (2009) 2.27
PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biol (2008) 2.22
ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat Biotechnol (2010) 2.22
MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. Anal Chem (2009) 2.17
Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS. J Exp Bot (2004) 2.10
XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem (2008) 2.10
MET-IDEA: data extraction tool for mass spectrometry-based metabolomics. Anal Chem (2006) 1.94
Efficient calculation of accurate masses of isotopic peaks. J Am Soc Mass Spectrom (2006) 1.85
Ultrahigh-speed calculation of isotope distributions. Anal Chem (1996) 1.85
Mass spectral metabonomics beyond elemental formula: chemical database querying by matching experimental with computational fragmentation spectra. Anal Chem (2008) 1.83
MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics (2008) 1.83
PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis. Anal Chem (2011) 1.78
Comparing similar spectra: from similarity index to spectral contrast angle. J Am Soc Mass Spectrom (2002) 1.78
Advances in structure elucidation of small molecules using mass spectrometry. Bioanal Rev (2010) 1.76
Ultrahigh-pressure reversed-phase liquid chromatography in packed capillary columns. Anal Chem (1997) 1.73
An efficient method to calculate the aggregated isotopic distribution and exact center-masses. J Am Soc Mass Spectrom (2012) 1.71
Current progress in computational metabolomics. Brief Bioinform (2007) 1.70
The impact of bacterial genomics on natural product research. Angew Chem Int Ed Engl (2005) 1.70
MathDAMP: a package for differential analysis of metabolite profiles. BMC Bioinformatics (2006) 1.68
SIRIUS: decomposing isotope patterns for metabolite identification. Bioinformatics (2008) 1.68
IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data. Bioinformatics (2012) 1.67
Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets. Bioinformatics (2011) 1.57
MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites. Plant J (2009) 1.55
A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. J Comput Biol (2001) 1.55
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. BMC Syst Biol (2011) 1.52
Analytical and statistical approaches to metabolomics research. J Sep Sci (2009) 1.52
FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data. Rapid Commun Mass Spectrom (2008) 1.51
Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics (2010) 1.51
Reduction of chemical formulas from the isotopic peak distributions of high-resolution mass spectra. Anal Chem (2003) 1.50
Wavelet- and Fourier-transform-based spectrum similarity approaches to compound identification in gas chromatography/mass spectrometry. Anal Chem (2011) 1.49
Chromatographic alignment by warping and dynamic programming as a pre-processing tool for PARAFAC modelling of liquid chromatography-mass spectrometry data. J Chromatogr A (2002) 1.48
Liquid chromatography/atmospheric pressure ionization-mass spectrometry in drug metabolism studies. J Mass Spectrom (2003) 1.47
MetExtract: a new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research. Bioinformatics (2012) 1.44
Visualizing plant metabolomic correlation networks using clique-metabolite matrices. Bioinformatics (2001) 1.44
Congruent strategies for carbohydrate sequencing. 2. FragLib: an MSn spectral library. Anal Chem (2005) 1.41
Dereplication and de novo sequencing of nonribosomal peptides. Nat Methods (2009) 1.41
TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. BMC Bioinformatics (2009) 1.40
Molecular formula and METLIN Personal Metabolite Database matching applied to the identification of compounds generated by LC/TOF-MS. J Biomol Tech (2008) 1.38
Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Anal Chem (2009) 1.37
Metabolite identification and molecular fingerprint prediction through machine learning. Bioinformatics (2012) 1.36
MALDI ionization: the role of in-plume processes. Chem Rev (2003) 1.36
Elemental formula annotation of polar and lipophilic metabolites using (13) C, (15) N and (34) S isotope labelling, in combination with high-resolution mass spectrometry. Plant J (2011) 1.35
Metabolite identification using automated comparison of high-resolution multistage mass spectral trees. Anal Chem (2012) 1.35
Computational mass spectrometry for metabolomics: identification of metabolites and small molecules. Anal Bioanal Chem (2010) 1.33
Towards de novo identification of metabolites by analyzing tandem mass spectra. Bioinformatics (2008) 1.31
Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry. Trends Analyt Chem (2008) 1.31
Feature trees: a new molecular similarity measure based on tree matching. J Comput Aided Mol Des (1998) 1.30
MetFusion: integration of compound identification strategies. J Mass Spectrom (2013) 1.30
A method of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry. Bioinformatics (2012) 1.27
Data analysis tool for comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry. Anal Chem (2011) 1.24
Metabolite identification and quantitation in LC-MS/MS-based metabolomics. Trends Analyt Chem (2012) 1.23
Probabilistic assignment of formulas to mass peaks in metabolomics experiments. Bioinformatics (2008) 1.22
Dissociation of individual isotopic peaks: predicting isotopic distributions of product ions in MSn. J Am Soc Mass Spectrom (2003) 1.22
X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry. Anal Chem (2009) 1.20
Mass spectrometry for the identification of the discriminating signals from metabolomics: current status and future trends. J Chromatogr B Analyt Technol Biomed Life Sci (2008) 1.19
MetSign: a computational platform for high-resolution mass spectrometry-based metabolomics. Anal Chem (2011) 1.19
Estimating probabilities of correct identification from results of mass spectral library searches. J Am Soc Mass Spectrom (1994) 1.18
Computing fragmentation trees from tandem mass spectrometry data. Anal Chem (2010) 1.18
Chemical substructure identification by mass spectral library searching. J Am Soc Mass Spectrom (1995) 1.17
AStream: an R package for annotating LC/MS metabolomic data. Bioinformatics (2011) 1.16
Stable isotope assisted assignment of elemental compositions for metabolomics. Anal Chem (2007) 1.16
GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA). BMC Bioinformatics (2011) 1.15
Determination of ion structures in structurally related compounds using precursor ion fingerprinting. J Am Soc Mass Spectrom (2008) 1.14
High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res (2004) 1.92
Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS. Nucleic Acids Res (2005) 1.49
Novel mass spectrometry-based tool for genotypic identification of mycobacteria. J Clin Microbiol (2004) 1.37
Computational mass spectrometry for metabolomics: identification of metabolites and small molecules. Anal Bioanal Chem (2010) 1.33
Comprehensive cluster analysis with Transitivity Clustering. Nat Protoc (2011) 1.28
Exact and heuristic algorithms for weighted cluster editing. Comput Syst Bioinformatics Conf (2007) 1.27
Partitioning biological data with transitivity clustering. Nat Methods (2010) 1.23
Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification. Proc Natl Acad Sci U S A (2002) 1.19
Computing fragmentation trees from tandem mass spectrometry data. Anal Chem (2010) 1.18
Unbiased transcriptional comparisons of generalist and specialist herbivores feeding on progressively defenseless Nicotiana attenuata plants. PLoS One (2010) 1.09
Identifying the unknowns by aligning fragmentation trees. Anal Chem (2012) 1.04
EPoS: a modular software framework for phylogenetic analysis. Bioinformatics (2008) 0.97
De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis (2009) 0.95
Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics. BMC Bioinformatics (2008) 0.93
Automated bond order assignment as an optimization problem. Bioinformatics (2011) 0.90
Finding maximum colorful subtrees in practice. J Comput Biol (2013) 0.88
Computing fragmentation trees from metabolite multiple mass spectrometry data. J Comput Biol (2011) 0.87
De novo analysis of electron impact mass spectra using fragmentation trees. Anal Chim Acta (2012) 0.86
SAMPI: protein identification with mass spectra alignments. BMC Bioinformatics (2007) 0.83
Mass spectrometry imaging of surface lipids on intact Drosophila melanogaster flies. J Mass Spectrom (2014) 0.83
Determination of ¹⁵N-incorporation into plant proteins and their absolute quantitation: a new tool to study nitrogen flux dynamics and protein pool sizes elicited by plant-herbivore interactions. J Proteome Res (2012) 0.82
New kids on the block: novel informatics methods for natural product discovery. Nat Prod Rep (2014) 0.81
Statistics for approximate gene clusters. BMC Bioinformatics (2013) 0.78
Fast alignment of fragmentation trees. Bioinformatics (2012) 0.78
Combinatorics of aliphatic amino acids. Naturwissenschaften (2010) 0.77
Analysis of different synthetic homopolymers by the use of a new calculation software for tandem mass spectra. Rapid Commun Mass Spectrom (2011) 0.76
Identifying gene clusters by discovering common intervals in indeterminate strings. BMC Genomics (2014) 0.76
Correction: Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina). PLoS Genet (2016) 0.75
Swiftly computing center strings. BMC Bioinformatics (2011) 0.75
Polynomial supertree methods revisited. Adv Bioinformatics (2011) 0.75
COCONUT—An Efficient Tool for Estimating Copolymer Compositions from Mass Spectra. Anal Chem (2015) 0.75
Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Sci Rep (2017) 0.75