-
1
-
-
84858790233
-
Innovation: metabolomics: the apogee of the omics trilogy
-
Patti G.J., Yanes O., Siuzdak G. Innovation: metabolomics: the apogee of the omics trilogy. Nat. Rev. Mol. Cell Biol 2012, 13:263-269. 10.1038/nrm3314.
-
(2012)
Nat. Rev. Mol. Cell Biol
, vol.13
, pp. 263-269
-
-
Patti, G.J.1
Yanes, O.2
Siuzdak, G.3
-
2
-
-
80051682403
-
Advances in metabolite identification
-
Wishart D.S. Advances in metabolite identification. Bioanalysis 2011, 3:1769-1782. 10.4155/bio.11.155.
-
(2011)
Bioanalysis
, vol.3
, pp. 1769-1782
-
-
Wishart, D.S.1
-
3
-
-
34748888866
-
Proposed minimum reporting standards for chemical analysis
-
Sumner L.W., Amberg A., Barrett D., Beale M.H., Beger R., Daykin C.A., et al. Proposed minimum reporting standards for chemical analysis. Metabolomics 2007, 3:211-221. 10.1007/s11306-007-0082-2.
-
(2007)
Metabolomics
, vol.3
, pp. 211-221
-
-
Sumner, L.W.1
Amberg, A.2
Barrett, D.3
Beale, M.H.4
Beger, R.5
Daykin, C.A.6
-
4
-
-
78650725285
-
Computational strategies for metabolite identification in metabolomics
-
Wishart D.S. Computational strategies for metabolite identification in metabolomics. Bioanalysis 2009, 1:1579-1596. 10.4155/bio.09.138.
-
(2009)
Bioanalysis
, vol.1
, pp. 1579-1596
-
-
Wishart, D.S.1
-
5
-
-
84907095098
-
Metabolite identification: are you sure? And how do your peers gauge your confidence?
-
Creek D.J., Dunn W.B., Fiehn O., Griffin J.L., Hall R.D., Lei Z., et al. Metabolite identification: are you sure? And how do your peers gauge your confidence?. Metabolomics 2014, 10:350-353. 10.1007/s11306-014-0656-8.
-
(2014)
Metabolomics
, vol.10
, pp. 350-353
-
-
Creek, D.J.1
Dunn, W.B.2
Fiehn, O.3
Griffin, J.L.4
Hall, R.D.5
Lei, Z.6
-
6
-
-
84922080318
-
Proposed quantitative and alphanumeric metabolite identification metrics
-
Sumner L., Lei Z., Nikolau B., Saito K., Roessner U., Trengove R. Proposed quantitative and alphanumeric metabolite identification metrics. Metabolomics 2014, 10:1047-1049. 10.1007/s11306-014-0739-6.
-
(2014)
Metabolomics
, vol.10
, pp. 1047-1049
-
-
Sumner, L.1
Lei, Z.2
Nikolau, B.3
Saito, K.4
Roessner, U.5
Trengove, R.6
-
7
-
-
84931565507
-
Embedding standards in metabolomics: the Metabolomics Society data standards task group
-
Salek R., Arita M., Dayalan S., Ebbels T., Jones A., Neumann S., et al. Embedding standards in metabolomics: the Metabolomics Society data standards task group. Metabolomics 2015, 11:782-783. 10.1007/s11306-015-0821-8.
-
(2015)
Metabolomics
, vol.11
, pp. 782-783
-
-
Salek, R.1
Arita, M.2
Dayalan, S.3
Ebbels, T.4
Jones, A.5
Neumann, S.6
-
8
-
-
34748839546
-
Proposed minimum reporting standards for data analysis in metabolomics
-
Goodacre R., Broadhurst D., Smilde A.K., Kristal B.S., Baker J.D., Beger R., et al. Proposed minimum reporting standards for data analysis in metabolomics. Metabolomics 2007, 3:231-241. 10.1007/s11306-007-0081-3.
-
(2007)
Metabolomics
, vol.3
, pp. 231-241
-
-
Goodacre, R.1
Broadhurst, D.2
Smilde, A.K.3
Kristal, B.S.4
Baker, J.D.5
Beger, R.6
-
9
-
-
84874345577
-
Mass appeal: Metabolite identification in mass spectrometry-focused untargeted metabolomics
-
Dunn W.B., Erban A., Weber R.J.M., Creek D.J., Brown M., Breitling R., et al. Mass appeal: Metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics 2013, 9:44-66. 10.1007/s11306-012-0434-4.
-
(2013)
Metabolomics
, vol.9
, pp. 44-66
-
-
Dunn, W.B.1
Erban, A.2
Weber, R.J.M.3
Creek, D.J.4
Brown, M.5
Breitling, R.6
-
10
-
-
62649105337
-
Identification of a new endogenous metabolite and the characterization of its protein interactions through an immobilization approach
-
Kalisiak J., Trauger S.A., Kalisiak E., Morita H., Fokin V.V., Adams M.W.W., et al. Identification of a new endogenous metabolite and the characterization of its protein interactions through an immobilization approach. J. Am. Chem. Soc 2009, 131:378-386. 10.1021/ja808172n.
-
(2009)
J. Am. Chem. Soc
, vol.131
, pp. 378-386
-
-
Kalisiak, J.1
Trauger, S.A.2
Kalisiak, E.3
Morita, H.4
Fokin, V.V.5
Adams, M.W.W.6
-
11
-
-
79953733693
-
Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease
-
Wang Z., Klipfell E., Bennett B.J., Koeth R., Levison B.S., Dugar B., et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 2011, 472:57-63. 10.1038/nature09922.
-
(2011)
Nature
, vol.472
, pp. 57-63
-
-
Wang, Z.1
Klipfell, E.2
Bennett, B.J.3
Koeth, R.4
Levison, B.S.5
Dugar, B.6
-
12
-
-
67649785231
-
How large is the metabolome? A critical analysis of data exchange practices in chemistry
-
Kind T., Scholz M., Fiehn O. How large is the metabolome? A critical analysis of data exchange practices in chemistry. PLoS ONE 2009, 4. 10.1371/journal.pone.0005440.
-
(2009)
PLoS ONE
, vol.4
-
-
Kind, T.1
Scholz, M.2
Fiehn, O.3
-
13
-
-
84866437252
-
Metabolite identification and molecular fingerprint prediction through machine learning
-
Heinonen M., Shen H., Zamboni N., Rousu J. Metabolite identification and molecular fingerprint prediction through machine learning. Bioinformatics 2012, 28:2333-2341. 10.1093/bioinformatics/bts437.
-
(2012)
Bioinformatics
, vol.28
, pp. 2333-2341
-
-
Heinonen, M.1
Shen, H.2
Zamboni, N.3
Rousu, J.4
-
14
-
-
84875154340
-
MetFusion: integration of compound identification strategies
-
Gerlich M., Neumann S. MetFusion: integration of compound identification strategies. J. Mass Spectrom 2013, 48:291-298. 10.1002/jms.3123.
-
(2013)
J. Mass Spectrom
, vol.48
, pp. 291-298
-
-
Gerlich, M.1
Neumann, S.2
-
15
-
-
84875432479
-
MyCompoundID: using an evidence-based metabolome library for metabolite identification
-
Li L., Li R., Zhou J., Zuniga A., Stanislaus A.E., Wu Y., et al. MyCompoundID: using an evidence-based metabolome library for metabolite identification. Anal. Chem 2013, 85:3401-3408. 10.1021/ac400099b.
-
(2013)
Anal. Chem
, vol.85
, pp. 3401-3408
-
-
Li, L.1
Li, R.2
Zhou, J.3
Zuniga, A.4
Stanislaus, A.E.5
Wu, Y.6
-
16
-
-
84904810329
-
CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra
-
Allen F., Pon A., Wilson M., Greiner R., Wishart D. CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Nucleic Acids Res 2014, 42. 10.1093/nar/gku436.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Allen, F.1
Pon, A.2
Wilson, M.3
Greiner, R.4
Wishart, D.5
-
17
-
-
84926363137
-
Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification
-
Allen F., Greiner R., Wishart D. Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification. Metabolomics 2014, 11:98-110. 10.1007/s11306-014-0676-4.
-
(2014)
Metabolomics
, vol.11
, pp. 98-110
-
-
Allen, F.1
Greiner, R.2
Wishart, D.3
-
18
-
-
84866362686
-
Substructure-based annotation of high-resolution multistage MSn spectral trees
-
Ridder L., Van Der Hooft J.J.J., Verhoeven S., De Vos R.C.H., Van Schaik R., Vervoort J. Substructure-based annotation of high-resolution multistage MSn spectral trees. Rapid Commun. Mass Spectrom 2012, 26:2461-2471. 10.1002/rcm.6364.
-
(2012)
Rapid Commun. Mass Spectrom
, vol.26
, pp. 2461-2471
-
-
Ridder, L.1
Van Der Hooft, J.J.J.2
Verhoeven, S.3
De Vos, R.C.H.4
Van Schaik, R.5
Vervoort, J.6
-
19
-
-
84879199446
-
Automatic chemical structure annotation of an LC - MS based metabolic profile from green tea
-
Ridder L., van der Hooft J., Verhoevem S., de Vos R.C.H., Bino R.J., Vervoort J. Automatic chemical structure annotation of an LC - MS based metabolic profile from green tea. Anal. Chem 2013, 85:6033-6040.
-
(2013)
Anal. Chem
, vol.85
, pp. 6033-6040
-
-
Ridder, L.1
van der Hooft, J.2
Verhoevem, S.3
de Vos, R.C.H.4
Bino, R.J.5
Vervoort, J.6
-
20
-
-
84878742600
-
Towards first principles calculation of electron impact mass spectra of molecules
-
Grimme S. Towards first principles calculation of electron impact mass spectra of molecules. Angew. Chem. Int. Ed. Engl 2013, 52:6306-6312. 10.1002/anie.201300158.
-
(2013)
Angew. Chem. Int. Ed. Engl
, vol.52
, pp. 6306-6312
-
-
Grimme, S.1
-
21
-
-
79959898098
-
Extending biochemical databases by metabolomic surveys
-
Fiehn O., Barupal D.K., Kind T. Extending biochemical databases by metabolomic surveys. J. Biol. Chem 2011, 286:23637-23643. 10.1074/jbc.R110.173617.
-
(2011)
J. Biol. Chem
, vol.286
, pp. 23637-23643
-
-
Fiehn, O.1
Barupal, D.K.2
Kind, T.3
-
22
-
-
0032919364
-
KEGG: kyoto encyclopedia of genes and genomes
-
Ogata H., Goto S., Sato K., Fujibuchi W., Bono H., Kanehisa M. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 1999, 27:29-34. 10.1093/nar/27.1.29.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
23
-
-
13444259844
-
Reactome: a knowledgebase of biological pathways
-
Joshi-Tope G., Gillespie M., Vastrik I., Eustachio P.D., Schmidt E., de Bono B., et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005, 33. 10.1093/nar/gki072.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Joshi-Tope, G.1
Gillespie, M.2
Vastrik, I.3
Eustachio, P.D.4
Schmidt, E.5
de Bono, B.6
-
24
-
-
84862203775
-
WikiPathways: building research communities on biological pathways
-
Kelder T., Van Iersel M.P., Hanspers K., Kutmon M., Conklin B.R., Evelo C.T., et al. WikiPathways: building research communities on biological pathways. Nucleic Acids Res 2012, 40. 10.1093/nar/gkr1074.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Kelder, T.1
Van Iersel, M.P.2
Hanspers, K.3
Kutmon, M.4
Conklin, B.R.5
Evelo, C.T.6
-
25
-
-
27244436714
-
Expansion of the Biocyc collection of pathway/genome databases to 160 genomes
-
Karp P.D., Ouzounis C.A., Moore-Kochlacs C., Goldovsky L., Kaipa P., Ahrén D., et al. Expansion of the Biocyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 2005, 33:6083-6089. 10.1093/nar/gki892.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 6083-6089
-
-
Karp, P.D.1
Ouzounis, C.A.2
Moore-Kochlacs, C.3
Goldovsky, L.4
Kaipa, P.5
Ahrén, D.6
-
26
-
-
67849104638
-
PubChem: a public information system for analyzing bioactivities of small molecules
-
Wang Y., Xiao J., Suzek T.O., Zhang J., Wang J., Bryant S.H. PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res 2009, 37. 10.1093/nar/gkp456.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Wang, Y.1
Xiao, J.2
Suzek, T.O.3
Zhang, J.4
Wang, J.5
Bryant, S.H.6
-
27
-
-
78449296488
-
Chemspider: an online chemical information resource
-
Pence H.E., Williams A. Chemspider: an online chemical information resource. J. Chem. Educ 2010, 87:1123-1124. 10.1021/ed100697w.
-
(2010)
J. Chem. Educ
, vol.87
, pp. 1123-1124
-
-
Pence, H.E.1
Williams, A.2
-
28
-
-
84875123279
-
Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database
-
Zhu Z.-J., Schultz A.W., Wang J., Johnson C.H., Yannone S.M., Patti G.J., et al. Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nat. Protoc 2013, 8:451-460. 10.1038/nprot.2013.004.
-
(2013)
Nat. Protoc
, vol.8
, pp. 451-460
-
-
Zhu, Z.-J.1
Schultz, A.W.2
Wang, J.3
Johnson, C.H.4
Yannone, S.M.5
Patti, G.J.6
-
29
-
-
77954439868
-
MassBank: a public repository for sharing mass spectral data for life sciences
-
Horai H., Arita M., Kanaya S., Nihei Y., Ikeda T., Suwa K., et al. MassBank: a public repository for sharing mass spectral data for life sciences. J. Mass Spectrom 2010, 45:703-714. 10.1002/jms.1777.
-
(2010)
J. Mass Spectrom
, vol.45
, pp. 703-714
-
-
Horai, H.1
Arita, M.2
Kanaya, S.3
Nihei, Y.4
Ikeda, T.5
Suwa, K.6
-
30
-
-
20244380782
-
GMD@CSB.DB: the golm metabolome database
-
Kopka J., Schauer N., Krueger S., Birkemeyer C., Usadel B., Bergmüller E., et al. GMD@CSB.DB: the golm metabolome database. Bioinformatics 2005, 21:1635-1638. 10.1093/bioinformatics/bti236.
-
(2005)
Bioinformatics
, vol.21
, pp. 1635-1638
-
-
Kopka, J.1
Schauer, N.2
Krueger, S.3
Birkemeyer, C.4
Usadel, B.5
Bergmüller, E.6
-
31
-
-
84876148784
-
HMDB 3.0-the human metabolome database in 2013
-
Wishart D.S., Jewison T., Guo A.C., Wilson M., Knox C., Liu Y., et al. HMDB 3.0-the human metabolome database in 2013. Nucleic Acids Res 2013, 41. 10.1093/nar/gks1065.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Wishart, D.S.1
Jewison, T.2
Guo, A.C.3
Wilson, M.4
Knox, C.5
Liu, Y.6
-
32
-
-
77951072181
-
Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer
-
Lu W., Clasquin M.F., Melamud E., Amador-Noguez D., Caudy A.A., Rabinowitz J.D. Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. Anal. Chem 2010, 82:3212-3221. 10.1021/ac902837x.
-
(2010)
Anal. Chem
, vol.82
, pp. 3212-3221
-
-
Lu, W.1
Clasquin, M.F.2
Melamud, E.3
Amador-Noguez, D.4
Caudy, A.A.5
Rabinowitz, J.D.6
-
33
-
-
32444446805
-
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification
-
Smith C.A., Want E.J., Maille G.O., Abagyan R., Siuzdak G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem 2006, 78:779-787. 10.1021/ac051437y.
-
(2006)
Anal. Chem
, vol.78
, pp. 779-787
-
-
Smith, C.A.1
Want, E.J.2
Maille, G.O.3
Abagyan, R.4
Siuzdak, G.5
-
34
-
-
65249132985
-
Metalign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing
-
Lommen A. Metalign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal. Chem 2009, 81:3079-3086. 10.1021/ac900036d.
-
(2009)
Anal. Chem
, vol.81
, pp. 3079-3086
-
-
Lommen, A.1
-
35
-
-
33644867564
-
MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data
-
Katajamaa M., Miettinen J., Oresic M. MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 2006, 22:634-636. 10.1093/bioinformatics/btk039.
-
(2006)
Bioinformatics
, vol.22
, pp. 634-636
-
-
Katajamaa, M.1
Miettinen, J.2
Oresic, M.3
-
36
-
-
77954772536
-
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
-
Pluskal T., Castillo S., Villar-Briones A., Oresic M. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 2010, 11:395. 10.1186/1471-2105-11-395.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 395
-
-
Pluskal, T.1
Castillo, S.2
Villar-Briones, A.3
Oresic, M.4
-
37
-
-
84885922460
-
A guideline to univariate statistical analysis for LC/MS-based untargeted metabolomics-derived data
-
accessed 01.02.16
-
Vinaixa M., Samino S., Saez I., Duran J., Guinovart J.J., Yanes O. A guideline to univariate statistical analysis for LC/MS-based untargeted metabolomics-derived data. Metabolites 2012, 2:775-795. accessed 01.02.16. http://www.mdpi.com/2218-1989/2/4/775.
-
(2012)
Metabolites
, vol.2
, pp. 775-795
-
-
Vinaixa, M.1
Samino, S.2
Saez, I.3
Duran, J.4
Guinovart, J.J.5
Yanes, O.6
-
38
-
-
84855402302
-
CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets
-
Kuhl C., Tautenhahn R., Böttcher C., Larson T.R., Neumann S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal. Chem 2012, 84:283-289. 10.1021/ac202450g.
-
(2012)
Anal. Chem
, vol.84
, pp. 283-289
-
-
Kuhl, C.1
Tautenhahn, R.2
Böttcher, C.3
Larson, T.R.4
Neumann, S.5
-
39
-
-
79954462033
-
AStream: an R package for annotating LC/MS metabolomic data
-
Alonso A., Julià A., Beltran A., Vinaixa M., Díaz M., Ibañez L., et al. AStream: an R package for annotating LC/MS metabolomic data. Bioinformatics 2011, 27:1339-1340. 10.1093/bioinformatics/btr138.
-
(2011)
Bioinformatics
, vol.27
, pp. 1339-1340
-
-
Alonso, A.1
Julià, A.2
Beltran, A.3
Vinaixa, M.4
Díaz, M.5
Ibañez, L.6
-
40
-
-
84957088655
-
-
accessed 18.05.15
-
Loos M. CRAN - package nontarget accessed 18.05.15. http://cran.r-project.org/web/packages/nontarget/index.html.
-
CRAN - package nontarget
-
-
Loos, M.1
-
41
-
-
79954519624
-
Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets
-
Brown M., Wedge D.C., Goodacre R., Kell D.B., Baker P.N., Kenny L.C., et al. Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets. Bioinformatics 2011, 27:1108-1112. 10.1093/bioinformatics/btr079.
-
(2011)
Bioinformatics
, vol.27
, pp. 1108-1112
-
-
Brown, M.1
Wedge, D.C.2
Goodacre, R.3
Kell, D.B.4
Baker, P.N.5
Kenny, L.C.6
-
42
-
-
84907929449
-
Comprehensive foodomics study on the mechanisms operating at various molecular levels in cancer cells in response to individual rosemary polyphenols
-
Valdés A., García-Cañas V., Simó C., Ibáñez C., Micol V., Ferragut J.A., et al. Comprehensive foodomics study on the mechanisms operating at various molecular levels in cancer cells in response to individual rosemary polyphenols. Anal. Chem 2014, 86:9807-9815. 10.1021/ac502401j.
-
(2014)
Anal. Chem
, vol.86
, pp. 9807-9815
-
-
Valdés, A.1
García-Cañas, V.2
Simó, C.3
Ibáñez, C.4
Micol, V.5
Ferragut, J.A.6
-
43
-
-
84864935209
-
CE/LC-MS multiplatform for broad metabolomic analysis of dietary polyphenols effect on colon cancer cells proliferation
-
Ibanez C., Simo C., Garcia-Canas V., Gomez-Martinez A., Ferragut J.A., Cifuentes A. CE/LC-MS multiplatform for broad metabolomic analysis of dietary polyphenols effect on colon cancer cells proliferation. Electrophoresis 2012, 33:2328-2336. 10.1002/elps.201200143.
-
(2012)
Electrophoresis
, vol.33
, pp. 2328-2336
-
-
Ibanez, C.1
Simo, C.2
Garcia-Canas, V.3
Gomez-Martinez, A.4
Ferragut, J.A.5
Cifuentes, A.6
-
44
-
-
84863085801
-
Global Foodomics strategy to investigate the health benefits of dietary constituents
-
Ibanez C., Valdes A., Garcia-Canas V., Simo C., Celebier M., Rocamora-Reverte L., et al. Global Foodomics strategy to investigate the health benefits of dietary constituents. J. Chromatogr. A 2012, 1248:139-153. 10.1016/j.chroma.2012.06.008.
-
(2012)
J. Chromatogr. A
, vol.1248
, pp. 139-153
-
-
Ibanez, C.1
Valdes, A.2
Garcia-Canas, V.3
Simo, C.4
Celebier, M.5
Rocamora-Reverte, L.6
-
45
-
-
33846088138
-
HMDB: the human metabolome database
-
Wishart D.S., Tzur D., Knox C., Eisner R., Guo A.C., Young N., et al. HMDB: the human metabolome database. Nucleic Acids Res 2007, 35:D521-D526. 10.1093/nar/gkl923.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D521-D526
-
-
Wishart, D.S.1
Tzur, D.2
Knox, C.3
Eisner, R.4
Guo, A.C.5
Young, N.6
-
46
-
-
38549127678
-
ChEBI: a database and ontology for chemical entities of biological interest
-
Degtyarenko K., De matos P., Ennis M., Hastings J., Zbinden M., Mcnaught A., et al. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 2008, 36. 10.1093/nar/gkm791.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Degtyarenko, K.1
De Matos, P.2
Ennis, M.3
Hastings, J.4
Zbinden, M.5
Mcnaught, A.6
-
47
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in
-
Boeckmann B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in. Nucleic Acids Res 2003, 31:365-370. 10.1093/nar/gkg095.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 365-370
-
-
Boeckmann, B.1
Bairoch, A.2
Apweiler, R.3
Blatter, M.C.4
Estreicher, A.5
Gasteiger, E.6
-
48
-
-
80053651587
-
GenBank
-
Benson D.A., Cavanaugh M., Clark K., Karsch-Mizrachi I., Lipman D.J., Ostell J., et al. GenBank. Nucleic Acids Res 2013, 41. 10.1093/nar/gks1195.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Benson, D.A.1
Cavanaugh, M.2
Clark, K.3
Karsch-Mizrachi, I.4
Lipman, D.J.5
Ostell, J.6
-
49
-
-
0033976454
-
GenBank
-
Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Rapp B.A., Wheeler D.L. GenBank. Nucleic Acids Res 2000, 28:15-18. 10.1093/nar/28.1.15.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 15-18
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Rapp, B.A.5
Wheeler, D.L.6
-
50
-
-
77249162211
-
Database resources in metabolomics: an overview
-
Go E.P. Database resources in metabolomics: an overview. J. Neuroimm. Pharmacol 2010, 5:18-30. 10.1007/s11481-009-9157-3.
-
(2010)
J. Neuroimm. Pharmacol
, vol.5
, pp. 18-30
-
-
Go, E.P.1
-
51
-
-
77952302069
-
In silico fragmentation for computer assisted identification of metabolite mass spectra
-
Wolf S., Schmidt S., Muller-Hannemann M., Neumann S. In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinform 2010, 11:148. 10.1186/1471-2105-11-148.
-
(2010)
BMC Bioinform
, vol.11
, pp. 148
-
-
Wolf, S.1
Schmidt, S.2
Muller-Hannemann, M.3
Neumann, S.4
-
52
-
-
78651082595
-
MzML - a community standard for mass spectrometry data
-
R110.000133
-
Martens L., Chambers M., Sturm M., Kessner D., Levander F., Shofstahl J., et al. mzML - a community standard for mass spectrometry data. Mol. Cell. Proteomics 2011, 10. R110.000133. 10.1074/mcp.R110.000133.
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Martens, L.1
Chambers, M.2
Sturm, M.3
Kessner, D.4
Levander, F.5
Shofstahl, J.6
-
53
-
-
32444432587
-
METLIN: a metabolite mass spectral database
-
Smith C.A., O'Maille G., Want E.J., Qin C., Trauger S.A., Brandon T.R., et al. METLIN: a metabolite mass spectral database. Ther. Drug Monit 2005, 27:747-751. 10.1097/01.ftd.0000179845.53213.39.
-
(2005)
Ther. Drug Monit
, vol.27
, pp. 747-751
-
-
Smith, C.A.1
O'Maille, G.2
Want, E.J.3
Qin, C.4
Trauger, S.A.5
Brandon, T.R.6
-
54
-
-
63449119987
-
Molecular formula and METLIN personal metabolite database matching applied to the identification of compounds generated by LC/TOF-MS
-
Sana T.R., Roark J.C., Li X., Waddell K., Fischer S.M. Molecular formula and METLIN personal metabolite database matching applied to the identification of compounds generated by LC/TOF-MS. J. Biomol. Tech 2008, 19:258-266.
-
(2008)
J. Biomol. Tech
, vol.19
, pp. 258-266
-
-
Sana, T.R.1
Roark, J.C.2
Li, X.3
Waddell, K.4
Fischer, S.M.5
-
55
-
-
70349125897
-
X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry
-
Mylonas R., Mauron Y., Masselot A., Binz P.-A., Budin N., Fathi M., et al. X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry. Anal. Chem 2009, 81:7604-7610. 10.1021/ac900954d.
-
(2009)
Anal. Chem
, vol.81
, pp. 7604-7610
-
-
Mylonas, R.1
Mauron, Y.2
Masselot, A.3
Binz, P.-A.4
Budin, N.5
Fathi, M.6
-
56
-
-
48349128711
-
-
accessed 18.05.15
-
MassBank Project | download accessed 18.05.15. http://www.massbank.jp/en/download.html.
-
| download
-
-
-
57
-
-
84872336476
-
Automatic recalibration and processing of tandem mass spectra using formula annotation
-
Stravs M.A., Schymanski E.L., Singer H.P., Hollender J. Automatic recalibration and processing of tandem mass spectra using formula annotation. J. Mass Spectrom 2013, 48:89-99. 10.1002/jms.3131.
-
(2013)
J. Mass Spectrom
, vol.48
, pp. 89-99
-
-
Stravs, M.A.1
Schymanski, E.L.2
Singer, H.P.3
Hollender, J.4
-
59
-
-
34249874435
-
The IUPAC international chemical identifier: InChI-A new standard for molecular informatics
-
McNaught A. The IUPAC international chemical identifier: InChI-A new standard for molecular informatics. Chem. Int 2006, 28:12-14. 10.1016/j.hrthm.2010.04.035.
-
(2006)
Chem. Int
, vol.28
, pp. 12-14
-
-
McNaught, A.1
-
61
-
-
80255133233
-
Lipid classification, structures and tools
-
Fahy E., Cotter D., Sud M., Subramaniam S. Lipid classification, structures and tools. Biochim. Biophys. Acta - Mol. Cell Biol. Lipids 2011, 1811:637-647. 10.1016/j.bbalip.2011.06.009.
-
(2011)
Biochim. Biophys. Acta - Mol. Cell Biol. Lipids
, vol.1811
, pp. 637-647
-
-
Fahy, E.1
Cotter, D.2
Sud, M.3
Subramaniam, S.4
-
62
-
-
84881476562
-
LipidBlast in silico tandem mass spectrometry database for lipid identification
-
Kind T., Liu K.H., do Lee Y., DeFelice B., Meissen J.K., Fiehn O. LipidBlast in silico tandem mass spectrometry database for lipid identification. Nat. Methods 2013, 10:755-758. 10.1038/nmeth.2551.
-
(2013)
Nat. Methods
, vol.10
, pp. 755-758
-
-
Kind, T.1
Liu, K.H.2
do Lee, Y.3
DeFelice, B.4
Meissen, J.K.5
Fiehn, O.6
-
63
-
-
84982278179
-
-
US Secretary of Commerce, Gaithersburg, Maryland, USA
-
National Institute of Standards and Technology NIST/EPA/NIH Mass Spectral Library v2014 2014, US Secretary of Commerce, Gaithersburg, Maryland, USA.
-
(2014)
NIST/EPA/NIH Mass Spectral Library v2014
-
-
-
64
-
-
84903722562
-
Quality control for building libraries from electrospray ionization tandem mass spectra
-
Yang X., Neta P., Stein S.E. Quality control for building libraries from electrospray ionization tandem mass spectra. Anal. Chem 2014, 86:6393-6400. 10.1021/ac500711m.
-
(2014)
Anal. Chem
, vol.86
, pp. 6393-6400
-
-
Yang, X.1
Neta, P.2
Stein, S.E.3
-
65
-
-
84865769818
-
Mass spectral reference libraries: an ever-expanding resource for chemical identification
-
Stein S. Mass spectral reference libraries: an ever-expanding resource for chemical identification. Anal. Chem 2012, 84:7274-7282. 10.1021/ac301205z.
-
(2012)
Anal. Chem
, vol.84
, pp. 7274-7282
-
-
Stein, S.1
-
66
-
-
84983899955
-
Kovats retention indices of selected hydrocarbons through C10 on bonded phase fused silica capillaries
-
Lubeck A.J., Sutton D.L. Kovats retention indices of selected hydrocarbons through C10 on bonded phase fused silica capillaries. J. High Resolut. Chromatogr. Chromatogr. Commun 1983, 328-332. 10.1002/jhrc.1240060612 accessed 18.05.15.
-
(1983)
J. High Resolut. Chromatogr. Chromatogr. Commun
, pp. 328-332
-
-
Lubeck, A.J.1
Sutton, D.L.2
-
67
-
-
72449186517
-
FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry
-
Kind T., Wohlgemuth G., do Lee Y., Lu Y., Palazoglu M., Shahbaz S., et al. FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal. Chem 2009, 81:10038-10048. 10.1021/ac9019522.
-
(2009)
Anal. Chem
, vol.81
, pp. 10038-10048
-
-
Kind, T.1
Wohlgemuth, G.2
do Lee, Y.3
Lu, Y.4
Palazoglu, M.5
Shahbaz, S.6
-
68
-
-
34250720628
-
Development of a database of gas chromatographic retention properties of organic compounds
-
Babushok V.I., Linstrom P.J., Reed J.J., Zenkevich I.G., Brown R.L., Mallard W.G., et al. Development of a database of gas chromatographic retention properties of organic compounds. J. Chromatogr. A 2007, 1157:414-421. 10.1016/j.chroma.2007.05.044.
-
(2007)
J. Chromatogr. A
, vol.1157
, pp. 414-421
-
-
Babushok, V.I.1
Linstrom, P.J.2
Reed, J.J.3
Zenkevich, I.G.4
Brown, R.L.5
Mallard, W.G.6
-
70
-
-
34548841428
-
The GOLM metabolome database: a database for GC-MS based metabolite profiling
-
Hummel J., Selbig J., Walther D., Kopka J. The GOLM metabolome database: a database for GC-MS based metabolite profiling. Top. Curr. Genet 2007, 18:75-95. 10.1007/4735_2007_0229.
-
(2007)
Top. Curr. Genet
, vol.18
, pp. 75-95
-
-
Hummel, J.1
Selbig, J.2
Walther, D.3
Kopka, J.4
-
71
-
-
34250836437
-
Estimation of Kovats retention indices using group contributions
-
Stein S.E., Babushok V.I., Brown R.L., Linstrom P.J. Estimation of Kovats retention indices using group contributions. J. Chem. Inf. Model 2007, 47:975-980. 10.1021/ci600548y.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 975-980
-
-
Stein, S.E.1
Babushok, V.I.2
Brown, R.L.3
Linstrom, P.J.4
-
72
-
-
0000429874
-
Chemical substructure identification by mass spectral library searching
-
Stein S.E. Chemical substructure identification by mass spectral library searching. J. Am. Soc. Mass Spectrom 1995, 6:644-655. 10.1016/1044-0305(95)00291-K.
-
(1995)
J. Am. Soc. Mass Spectrom
, vol.6
, pp. 644-655
-
-
Stein, S.E.1
-
73
-
-
0001144659
-
Mass spectral classifiers for supporting systematic structure elucidation
-
Varmuza K., Werther W. Mass spectral classifiers for supporting systematic structure elucidation. J. Chem. Inf. Model 1996, 36:323-333. 10.1021/ci9501406.
-
(1996)
J. Chem. Inf. Model
, vol.36
, pp. 323-333
-
-
Varmuza, K.1
Werther, W.2
-
74
-
-
0028125717
-
Classification of mass spectra
-
Werther W., Lohninger H., Stancl F., Varmuza K. Classification of mass spectra. Chemom. Intell. Lab. Syst 1994, 22:63-76. 10.1016/0169-7439(94)85018-6.
-
(1994)
Chemom. Intell. Lab. Syst
, vol.22
, pp. 63-76
-
-
Werther, W.1
Lohninger, H.2
Stancl, F.3
Varmuza, K.4
-
75
-
-
79954566035
-
Decision tree supported substructure prediction of metabolites from GC-MS profiles
-
Hummel J., Strehmel N., Selbig J., Walther D., Kopka J. Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics 2010, 6:322-333. 10.1007/s11306-010-0198-7.
-
(2010)
Metabolomics
, vol.6
, pp. 322-333
-
-
Hummel, J.1
Strehmel, N.2
Selbig, J.3
Walther, D.4
Kopka, J.5
-
76
-
-
72449186517
-
FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry
-
Kind T., Wohlgemuth G., Lee D.Y., Lu Y., Palazoglu M., Shahbaz S., et al. FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal. Chem 2009, 81:10038-10048. 10.1021/ac9019522.
-
(2009)
Anal. Chem
, vol.81
, pp. 10038-10048
-
-
Kind, T.1
Wohlgemuth, G.2
Lee, D.Y.3
Lu, Y.4
Palazoglu, M.5
Shahbaz, S.6
-
77
-
-
79961123585
-
The volatile compound BinBase mass spectral database
-
Skogerson K., Wohlgemuth G., Barupal D.K., Fiehn O. The volatile compound BinBase mass spectral database. BMC Bioinform 2011, 12:321. 10.1186/1471-2105-12-321.
-
(2011)
BMC Bioinform
, vol.12
, pp. 321
-
-
Skogerson, K.1
Wohlgemuth, G.2
Barupal, D.K.3
Fiehn, O.4
-
78
-
-
67649834742
-
Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics
-
Brown M., Dunn W.B., Dobson P., Patel Y., Winder C.L., Francis-McIntyre S., et al. Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics. Analyst 2009, 134:1322-1332. 10.1039/b901179j.
-
(2009)
Analyst
, vol.134
, pp. 1322-1332
-
-
Brown, M.1
Dunn, W.B.2
Dobson, P.3
Patel, Y.4
Winder, C.L.5
Francis-McIntyre, S.6
-
79
-
-
77957759689
-
The Chemical Translation Service - a web-based tool to improve standardization of metabolomic reports
-
Wohlgemuth G., Haldiya P.K., Willighagen E., Kind T., Fiehn O. The Chemical Translation Service - a web-based tool to improve standardization of metabolomic reports. Bioinformatics 2010, 26:2647-2648. 10.1093/bioinformatics/btq476.
-
(2010)
Bioinformatics
, vol.26
, pp. 2647-2648
-
-
Wohlgemuth, G.1
Haldiya, P.K.2
Willighagen, E.3
Kind, T.4
Fiehn, O.5
-
80
-
-
0033429735
-
Unknown identification using reference mass spectra. Quality evaluation of databases
-
McLafferty F.W., Stauffer D.A., Loh S.Y., Wesdemiotis C. Unknown identification using reference mass spectra. Quality evaluation of databases. J. Am. Soc. Mass Spectrom 1999, 10:1229-1240. 10.1016/S1044-0305(99)00104-X.
-
(1999)
J. Am. Soc. Mass Spectrom
, vol.10
, pp. 1229-1240
-
-
McLafferty, F.W.1
Stauffer, D.A.2
Loh, S.Y.3
Wesdemiotis, C.4
-
82
-
-
65649117746
-
On the inter-instrument and inter-laboratory transferability of a tandem mass spectral reference library: 1. Results of an Austrian multicenter study
-
Oberacher H., Pavlic M., Libiseller K., Schubert B., Sulyok M., Schuhmacher R., et al. On the inter-instrument and inter-laboratory transferability of a tandem mass spectral reference library: 1. Results of an Austrian multicenter study. J. Mass Spectrom 2009, 44:485-493. 10.1002/jms.1545.
-
(2009)
J. Mass Spectrom
, vol.44
, pp. 485-493
-
-
Oberacher, H.1
Pavlic, M.2
Libiseller, K.3
Schubert, B.4
Sulyok, M.5
Schuhmacher, R.6
-
83
-
-
0000881748
-
Optimization and testing of mass spectral library search algorithms for compound identification
-
Stein S.E., Scott D.R. Optimization and testing of mass spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom 1994, 5:859-866. 10.1016/1044-0305(94)87009-8.
-
(1994)
J. Am. Soc. Mass Spectrom
, vol.5
, pp. 859-866
-
-
Stein, S.E.1
Scott, D.R.2
-
84
-
-
26444491700
-
Setup and annotation of metabolomic experiments by integrating biological and mass spectrometric metadata
-
Fiehn O., Wohlgemuth G., Sholz M. Setup and annotation of metabolomic experiments by integrating biological and mass spectrometric metadata. DILS 2005, 224-239. 10.1007/11530084.
-
(2005)
DILS
, pp. 224-239
-
-
Fiehn, O.1
Wohlgemuth, G.2
Sholz, M.3
-
85
-
-
84937761254
-
Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from salinispora species
-
Duncan K.R., Crüsemann M., Lechner A., Sarkar A., Li J., Ziemert N., et al. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from salinispora species. Chem. Biol 2015, 22:460-471. 10.1016/j.chembiol.2015.03.010.
-
(2015)
Chem. Biol
, vol.22
, pp. 460-471
-
-
Duncan, K.R.1
Crüsemann, M.2
Lechner, A.3
Sarkar, A.4
Li, J.5
Ziemert, N.6
-
86
-
-
84876560030
-
MetaboLights - an open-access general-purpose repository for metabolomics studies and associated meta-data
-
D781-6
-
Haug K., Salek R.M., Conesa P., Hastings J., de Matos P., Rijnbeek M., et al. MetaboLights - an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucl. Acids Res 2013, 41(Database issue):D781-6. 10.1093/nar/gks1004.
-
(2013)
Nucl. Acids Res
, vol.41
, Issue.DATABASE ISSUE
-
-
Haug, K.1
Salek, R.M.2
Conesa, P.3
Hastings, J.4
de Matos, P.5
Rijnbeek, M.6
-
87
-
-
85006210853
-
The role of reporting standards for metabolite annotation and identification in metabolomic studies
-
Salek R.M., Steinbeck C., Viant M.R., Goodacre R., Dunn W.B. The role of reporting standards for metabolite annotation and identification in metabolomic studies. Gigascience 2013, 2:13. 10.1186/2047-217X-2-13.
-
(2013)
Gigascience
, vol.2
, pp. 13
-
-
Salek, R.M.1
Steinbeck, C.2
Viant, M.R.3
Goodacre, R.4
Dunn, W.B.5
-
88
-
-
84907888159
-
IsoMETLIN: a database for isotope-based metabolomics
-
Cho K., Mahieu N., Ivanisevic J., Uritboonthai W., Chen Y.-J., Siuzdak G., et al. isoMETLIN: a database for isotope-based metabolomics. Anal. Chem 2014, 86:9358-9361. 10.1021/ac5029177.
-
(2014)
Anal. Chem
, vol.86
, pp. 9358-9361
-
-
Cho, K.1
Mahieu, N.2
Ivanisevic, J.3
Uritboonthai, W.4
Chen, Y.-J.5
Siuzdak, G.6
-
89
-
-
84910657003
-
Development of a GC/Quadrupole-Orbitrap mass spectrometer, part I: design and characterization
-
Peterson A.C., Hauschild J.-P., Quarmby S.T., Krumwiede D., Lange O., Lemke R.A.S., et al. Development of a GC/Quadrupole-Orbitrap mass spectrometer, part I: design and characterization. Anal. Chem 2014, 86:10036-10043. 10.1021/ac5014767.
-
(2014)
Anal. Chem
, vol.86
, pp. 10036-10043
-
-
Peterson, A.C.1
Hauschild, J.-P.2
Quarmby, S.T.3
Krumwiede, D.4
Lange, O.5
Lemke, R.A.S.6
-
90
-
-
84910663296
-
Development of a GC/Quadrupole-Orbitrap mass spectrometer, part II: new approaches for discovery metabolomics
-
Peterson A.C., Balloon A.J., Westphall M.S., Coon J.J. Development of a GC/Quadrupole-Orbitrap mass spectrometer, part II: new approaches for discovery metabolomics. Anal. Chem 2014, 86:10044-10051. 10.1021/ac5014755.
-
(2014)
Anal. Chem
, vol.86
, pp. 10044-10051
-
-
Peterson, A.C.1
Balloon, A.J.2
Westphall, M.S.3
Coon, J.J.4
-
91
-
-
84957429490
-
Annotating unknown components from GC/EI-MS-based metabolite profiling experiments using GC/APCI(+)-QTOFMS
-
Strehmel N., Kopka J., Scheel D., Böttcher C. Annotating unknown components from GC/EI-MS-based metabolite profiling experiments using GC/APCI(+)-QTOFMS. Metabolomics 2013, 10:324-336. 10.1007/s11306-013-0569-y.
-
(2013)
Metabolomics
, vol.10
, pp. 324-336
-
-
Strehmel, N.1
Kopka, J.2
Scheel, D.3
Böttcher, C.4
-
92
-
-
84957093889
-
-
accessed 01.02.2016
-
Thermo Scientific LipidSearchTM Software accessed 01.02.2016. http://www.thermoscientific.com/content/tfs/en/product/lipidsearch-software.html.
-
LipidSearchTM Software
-
-
-
95
-
-
84868018748
-
MaConDa: a publicly accessible mass spectrometry contaminants database
-
Weber R.J.M., Li E., Bruty J., He S., Viant M.R. MaConDa: a publicly accessible mass spectrometry contaminants database. Bioinformatics 2012, 28:2856-2857. 10.1093/bioinformatics/bts527.
-
(2012)
Bioinformatics
, vol.28
, pp. 2856-2857
-
-
Weber, R.J.M.1
Li, E.2
Bruty, J.3
He, S.4
Viant, M.R.5
-
96
-
-
84865247010
-
RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database
-
Sawada Y., Nakabayashi R., Yamada Y., Suzuki M., Sato M., Sakata A., et al. RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database. Phytochemistry 2012, 82:38-45. 10.1016/j.phytochem.2012.07.007.
-
(2012)
Phytochemistry
, vol.82
, pp. 38-45
-
-
Sawada, Y.1
Nakabayashi, R.2
Yamada, Y.3
Suzuki, M.4
Sato, M.5
Sakata, A.6
|