Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics (Q35715135)

9 August 2017

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

1 reference

9 August 2017

1 reference

2

1 reference

9 August 2017

1

Arpana Vaniya

1 reference

9 August 2017

1 June 2015

1 reference

Trends in Analytical Chemistry

9 August 2017

1 reference

9 August 2017

69

1 reference

9 August 2017

52-61

1 reference

Novel strategy for the determination of illegal adulterants in health foods and herbal medicines using high-performance liquid chromatography with high-resolution mass spectrometry

9 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

MS2Analyzer: A software for small molecule substructure annotations from accurate tandem mass spectra

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

MIDAS: a database-searching algorithm for metabolite identification in metabolomics.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Development and in silico evaluation of large-scale metabolite identification methods using functional group detection for metabolomics.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Computational analyses of spectral trees from electrospray multi-stage mass spectrometry to aid metabolite identification

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Molecular Formula Identification with SIRIUS.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Metabolite Identification through Machine Learning- Tackling CASMI Challenge Using FingerID

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Small Molecule Identification with MOLGEN and Mass Spectrometry

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

CASMI: And the Winner is . .

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Metabolite identification through multiple kernel learning on fragmentation trees

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

A metabolomics investigation of non-genotoxic carcinogenicity in the rat.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Proposed minimum reporting standards for chemical analysis

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

LipidBlast in silico tandem mass spectrometry database for lipid identification

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

A branched biosynthetic pathway is involved in production of roquefortine and related compounds in Penicillium chrysogenum.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

MetFusion: integration of compound identification strategies

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Computational mass spectrometry for small molecules

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Automated pipeline for de novo metabolite identification using mass-spectrometry-based metabolomics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Automatic recalibration and processing of tandem mass spectra using formula annotation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

MetiTree: a web application to organize and process high-resolution multi-stage mass spectrometry metabolomics data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

De novo analysis of electron impact mass spectra using fragmentation trees

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Metabolite identification and molecular fingerprint prediction through machine learning.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Fast alignment of fragmentation trees

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Identifying the Unknowns by Aligning Fragmentation Trees

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Computing fragmentation trees from metabolite multiple mass spectrometry data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Elemental composition determination based on MSn

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Cytotoxic veraguamides, alkynyl bromide-containing cyclic depsipeptides from the marine cyanobacterium cf. Oscillatoria margaritifera.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Identification of "known unknowns" utilizing accurate mass data and chemical abstracts service databases

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Tandem mass spectrometry strategies for phosphoproteome analysis.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Advances in structure elucidation of small molecules using mass spectrometry

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Computing fragmentation trees from tandem mass spectrometry data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Computational mass spectrometry for metabolomics: identification of metabolites and small molecules

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

In vitro and in vivo enzymatic syntheses and mass spectrometric database for N-glycans and o-glycans

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

In silico fragmentation for computer assisted identification of metabolite mass spectra

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Artifacts in Fourier transform mass spectrometry

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Carbohydrate structural isomers analyzed by sequential mass spectrometry

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Characterization of typical chemical background interferences in atmospheric pressure ionization liquid chromatography-mass spectrometry

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Metabolomics reviewed: a new "omics" platform technology for systems biology and implications for natural products research.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Congruent strategies for carbohydrate sequencing. 2. FragLib: an MSn spectral library

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

The evolving role of natural products in drug discovery

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Analysis of highly polar compounds of plant origin: combination of hydrophilic interaction chromatography and electrospray ion trap mass spectrometry.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Rapid structure elucidation of catecholamine conjugates with tandem mass spectrometry.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Identification of the chemical components of Saussurea involucrata by high-resolution mass spectrometry and the mass spectral trees similarity filter technique

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Identification tree based on fragmentation rules for structure elucidation of organophosphorus esters by electrospray mass spectrometry.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Finding maximum colorful subtrees in practice

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Substructure-based annotation of high-resolution multistage MS(n) spectral trees.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Fragmentation trees for the structural characterisation of metabolites

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Highly accurate chemical formula prediction tool utilizing high-resolution mass spectra, MS/MS fragmentation, heuristic rules, and isotope pattern matching.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Structural annotation and elucidation of conjugated phenolic compounds in black, green, and white tea extracts.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Automated lipid A structure assignment from hierarchical tandem mass spectrometry data

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Insights into chemotaxonomic composition and carbon cycling of phototrophic communities in an artesian sulfur-rich spring (Zodletone, Oklahoma, USA), a possible analog for ancient microbial mat systems.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

A statistically rigorous test for the identification of parent-fragment pairs in LC-MS datasets

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Complementary precursor ion and neutral loss scan mode tandem mass spectrometry for the analysis of glycerophosphatidylethanolamine lipids from whole rat retina.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Towards de novo identification of metabolites by analyzing tandem mass spectra

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Structure characterization of flavonoid O-diglycosides by positive and negative nano-electrospray ionization ion trap mass spectrometry

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Determination of flavone, flavonol, and flavanone aglycones by negative ion liquid chromatography electrospray ion trap mass spectrometry

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

A strategy for fast structural elucidation of metabolites in small volume plant extracts using automated MS-guided LC-MS-SPE-NMR

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4509603

Metabolite identification: are you sure? And how do your peers gauge your confidence?

23 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

Automated classification of candidate structures for computer-assisted structure elucidation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

Computer-assisted structure elucidation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

COMPUTER-ASSISTED STRUCTURE ELUCIDATION

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

Profiling taxanes in Taxus extracts using lc/ms and lc/ms/ms techniques

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

Evaluation of quadrupole time-of-flight tandem mass spectrometry and ion-trap multiple-stage mass spectrometry for the differentiation of C-glycosidic flavonoid isomers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

Characterization and identification of isomeric flavonoid O-diglycosides from genus Citrus in negative electrospray ionization by ion trap mass spectrometry and time-of-flight mass spectrometry

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

High-throughput, nontargeted metabolite fingerprinting using nominal mass flow injection electrospray mass spectrometry

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

Structural elucidation of low abundant metabolites in complex sample matrices

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

Spectral trees as a robust annotation tool in LC–MS based metabolomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

Winners of CASMI2013: Automated Tools and Challenge Data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

Molecular Formula Identification Using Isotope Pattern Analysis and Calculation of Fragmentation Trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

MOLecular structure GENeration with MOLGEN, new features and future developments

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.TRAC.2015.04.002

Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa

7 January 2021

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26213431

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Computational mass spectrometry for small-molecule fragmentation

1 reference

5 May 2024

https://opencitations.net/index/api/v1/citations/10.1016/J.TRAC.2013.09.008

Fragmentation trees reloaded

1 reference

5 May 2024

https://opencitations.net/index/api/v1/citations/10.1186/S13321-016-0116-8

Identifiers

DOI

10.1016/J.TRAC.2015.04.002

1 reference

9 August 2017

1 reference

9 August 2017

1 reference

PubMed ID

26213431