메뉴 건너뛰기




Volumn 11, Issue 1, 2015, Pages 98-110

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

Author keywords

Machine learning; Metabolite identification; MS MS; Tandem mass spectrometry

Indexed keywords


EID: 84926363137     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-014-0676-4     Document Type: Article
Times cited : (334)

References (42)
  • 1
    • 49549101405 scopus 로고    scopus 로고
    • Towards de novo identification of metabolites by analyzing tandem mass spectra
    • PID: 18689839
    • Böcker, S., & Rasche, F. (2008). Towards de novo identification of metabolites by analyzing tandem mass spectra. Bioinformatics, 24(16), i49–i55.
    • (2008) Bioinformatics , vol.24 , Issue.16 , pp. i49-i55
    • Böcker, S.1    Rasche, F.2
  • 2
    • 54949108677 scopus 로고    scopus 로고
    • Bolton, E., Wang, Y., Thiessen, P., & Bryant, S. (2008). PubChem: Integrated platform of small molecules and biological activities. In Chapeter 12 in Annual reports in computational chemistry (Vol. 4). Washington, DC: American Chemical Society
    • Bolton, E., Wang, Y., Thiessen, P., & Bryant, S. (2008). PubChem: Integrated platform of small molecules and biological activities. In Chapeter 12 in Annual reports in computational chemistry (Vol. 4). Washington, DC: American Chemical Society.
  • 5
    • 0000695960 scopus 로고
    • On a least squares adjustment of a sampled frequency table when the expected marginal totals are known
    • Deming, S., & Stephan, W. (1940). On a least squares adjustment of a sampled frequency table when the expected marginal totals are known. Annals of Mathematical Statistics, 11(4), 427–444.
    • (1940) Annals of Mathematical Statistics , vol.11 , Issue.4 , pp. 427-444
    • Deming, S.1    Stephan, W.2
  • 7
    • 16244402990 scopus 로고    scopus 로고
    • Metabolomics: Current analytical platforms and methodologies
    • COI: 1:CAS:528:DC%2BD2MXivVKru74%3D
    • Dunn, W. B., & Ellis, D. I. (2005). Metabolomics: Current analytical platforms and methodologies. Trends in Anal Chem, 24(4), 285–294.
    • (2005) Trends in Anal Chem , vol.24 , Issue.4 , pp. 285-294
    • Dunn, W.B.1    Ellis, D.I.2
  • 8
    • 0000857494 scopus 로고
    • An approach to correlate Tandem mass spectral data of peptides with amino acid sequences in a protein database
    • COI: 1:CAS:528:DyaK2MXhvF2htLw%3D, PID: 24226387
    • Eng, J. K., McCormack, A. L., & Yates, J. R. (1994). An approach to correlate Tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry, 5(11), 976–989.
    • (1994) Journal of the American Society for Mass Spectrometry , vol.5 , Issue.11 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 9
    • 0036007687 scopus 로고    scopus 로고
    • Metabolomics-the link between genotypes and phenotypes
    • COI: 1:CAS:528:DC%2BD38Xht1Kqtr0%3D, PID: 11860207
    • Fiehn, O. (2002). Metabolomics-the link between genotypes and phenotypes. Plant Molecular Biology, 48(1–2), 155–171.
    • (2002) Plant Molecular Biology , vol.48 , Issue.1-2 , pp. 155-171
    • Fiehn, O.1
  • 10
    • 84876234443 scopus 로고    scopus 로고
    • A predictive science approach to aid understanding of electrospray ionisation tandem mass spectrometric fragmentation pathways of small molecules using density functional calculations
    • COI: 1:CAS:528:DC%2BC3sXlvFWgt7Y%3D
    • Galezowska, A., Harrison, M. W., Herniman, J. M., Skylaris, C. K., & Langley, G. J. (2013). A predictive science approach to aid understanding of electrospray ionisation tandem mass spectrometric fragmentation pathways of small molecules using density functional calculations. Rapid Communications in Mass Spectrometry (RCM), 27(9), 964–970.
    • (2013) Rapid Communications in Mass Spectrometry (RCM) , vol.27 , Issue.9 , pp. 964-970
    • Galezowska, A.1    Harrison, M.W.2    Herniman, J.M.3    Skylaris, C.K.4    Langley, G.J.5
  • 11
    • 49149147973 scopus 로고
    • Iterative partial equalization of orbital electronegativity: A rapid access to atomic charges
    • COI: 1:CAS:528:DyaL3MXhslCjtbs%3D
    • Gasteiger, J., & Marsili, M. (1980). Iterative partial equalization of orbital electronegativity: A rapid access to atomic charges. Tetrahedron, 36(22), 3219–3228.
    • (1980) Tetrahedron , vol.36 , Issue.22 , pp. 3219-3228
    • Gasteiger, J.1    Marsili, M.2
  • 13
    • 84876560358 scopus 로고    scopus 로고
    • The ChEBI reference database and ontology for biologically relevant chemistry: Enhancements for 2013
    • Hastings, J., de Matos, P., & Dekker, A. (2013). The ChEBI reference database and ontology for biologically relevant chemistry: Enhancements for 2013. Nucleic Acids Research, 41(Database issue), D456–D463.
    • (2013) Nucleic Acids Research , vol.41 , Issue.Database issue , pp. D456-D463
    • Hastings, J.1    de Matos, P.2    Dekker, A.3
  • 14
    • 56149101337 scopus 로고    scopus 로고
    • FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data
    • COI: 1:CAS:528:DC%2BD1cXht1ekt7nI, PID: 18763276
    • Heinonen, M., Rantanen, A., Mielikainen, T., et al. (2008). FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data. Rapid Communications in Mass Spectrometry, 22, 3043–3052.
    • (2008) Rapid Communications in Mass Spectrometry , vol.22 , pp. 3043-3052
    • Heinonen, M.1    Rantanen, A.2    Mielikainen, T.3
  • 15
    • 84866437252 scopus 로고    scopus 로고
    • Metabolite identification and molecular fingerprint prediction through machine learning
    • COI: 1:CAS:528:DC%2BC38XhtlantbjM, PID: 22815355
    • Heinonen, M., Shen, H., Zamboni, N., & Rousu, J. (2012). Metabolite identification and molecular fingerprint prediction through machine learning. Bioinformatics, 28(18), 2333–2341.
    • (2012) Bioinformatics , vol.28 , Issue.18 , pp. 2333-2341
    • Heinonen, M.1    Shen, H.2    Zamboni, N.3    Rousu, J.4
  • 16
    • 27544443321 scopus 로고    scopus 로고
    • Automated assignment of high-resolution collisionally activated dissociation mass spectra using a systematic bond disconnection approach
    • COI: 1:CAS:528:DC%2BD2MXht1eht7jF
    • Hill, A. W., & Mortishire-Smith, R. J. (2005). Automated assignment of high-resolution collisionally activated dissociation mass spectra using a systematic bond disconnection approach. Rapid Communications in Mass Spectrometry, 19(21), 3111–3118.
    • (2005) Rapid Communications in Mass Spectrometry , vol.19 , Issue.21 , pp. 3111-3118
    • Hill, A.W.1    Mortishire-Smith, R.J.2
  • 17
    • 77954439868 scopus 로고    scopus 로고
    • MassBank: A public repository for sharing mass spectral data for life sciences
    • COI: 1:CAS:528:DC%2BC3cXovVCgsLg%3D, PID: 20623627
    • Horai, H., Arita, M., Kanaya, S., et al. (2010). MassBank: A public repository for sharing mass spectral data for life sciences. Journal of Mass Spectrometry, 45(7), 703–714.
    • (2010) Journal of Mass Spectrometry , vol.45 , Issue.7 , pp. 703-714
    • Horai, H.1    Arita, M.2    Kanaya, S.3
  • 18
    • 84888191935 scopus 로고    scopus 로고
    • Computational mass spectrometry for small-molecule fragmentation
    • COI: 1:CAS:528:DC%2BC3sXhvFyltr7J
    • Hufsky, F., Scheubert, K., & Böcker, S. (2014). Computational mass spectrometry for small-molecule fragmentation. Trends in Analytical Chemistry, 53, 41–48.
    • (2014) Trends in Analytical Chemistry , vol.53 , pp. 41-48
    • Hufsky, F.1    Scheubert, K.2    Böcker, S.3
  • 19
    • 33644874819 scopus 로고    scopus 로고
    • From genomics to chemical genomics: New developments in KEGG
    • COI: 1:CAS:528:DC%2BD28XisFyitw%3D%3D, PID: 16381885
    • Kanehisa, M., Goto, S., Hattori, M., et al. (2006). From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Research, 34, D354–D357.
    • (2006) Nucleic Acids Research , vol.34 , pp. D354-D357
    • Kanehisa, M.1    Goto, S.2    Hattori, M.3
  • 20
    • 84864008587 scopus 로고    scopus 로고
    • In silico identification software (ISIS): A machine learning approach to tandem mass spectral identification of lipids
    • COI: 1:CAS:528:DC%2BC38XptF2htrY%3D, PID: 22592377
    • Kangas, L. J., Metz, T. O., Isaac, G., Schrom, B. T., Ginovska-Pangovska, B., Wang, L., et al. (2012). In silico identification software (ISIS): A machine learning approach to tandem mass spectral identification of lipids. Bioinformatics, 28(13), 1705–1713.
    • (2012) Bioinformatics , vol.28 , Issue.13 , pp. 1705-1713
    • Kangas, L.J.1    Metz, T.O.2    Isaac, G.3    Schrom, B.T.4    Ginovska-Pangovska, B.5    Wang, L.6
  • 21
    • 34347405493 scopus 로고    scopus 로고
    • Data processing for mass spectrometry-based metabolomics
    • COI: 1:CAS:528:DC%2BD2sXnsFylsb8%3D, PID: 17466315
    • Katajamaa, M., & Oresic, M. (2007). Data processing for mass spectrometry-based metabolomics. Journal of Chromatography A, 1158(1–2), 318–328.
    • (2007) Journal of Chromatography A , vol.1158 , Issue.1-2 , pp. 318-328
    • Katajamaa, M.1    Oresic, M.2
  • 22
    • 33846435744 scopus 로고    scopus 로고
    • CASE via MS: Ranking structure candidates by mass spectra
    • COI: 1:CAS:528:DC%2BD2sXit1GjtA%3D%3D
    • Kerber, A., Meringer, M., & Rücker, C. (2006). CASE via MS: Ranking structure candidates by mass spectra. Croatica Chemica Acta, 79(3), 449–464.
    • (2006) Croatica Chemica Acta , vol.79 , Issue.3 , pp. 449-464
    • Kerber, A.1    Meringer, M.2    Rücker, C.3
  • 23
    • 78650737804 scopus 로고    scopus 로고
    • Advances in structure elucidation of small molecules using mass spectrometry
    • PID: 21289855
    • Kind, T., & Fiehn, O. (2010). Advances in structure elucidation of small molecules using mass spectrometry. Bioanalytical Reviews, 2(1–4), 23–60.
    • (2010) Bioanalytical Reviews , vol.2 , Issue.1-4 , pp. 23-60
    • Kind, T.1    Fiehn, O.2
  • 25
    • 34547888313 scopus 로고    scopus 로고
    • Even-electron ions: A systematic study of the neutral species lost in the dissociation of quasi-molecular ions
    • COI: 1:CAS:528:DC%2BD2sXpsVGmsbg%3D
    • Levsen, K., Schiebel, H. M., et al. (2007). Even-electron ions: A systematic study of the neutral species lost in the dissociation of quasi-molecular ions. Journal of Mass Spectrometry (JMS), 42, 1024–1044.
    • (2007) Journal of Mass Spectrometry (JMS) , vol.42 , pp. 1024-1044
    • Levsen, K.1    Schiebel, H.M.2
  • 27
    • 0141989734 scopus 로고    scopus 로고
    • PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry
    • COI: 1:CAS:528:DC%2BD3sXotlGnurs%3D, PID: 14558135
    • Ma, B., Zhang, K., Hendrie, C., Liang, C., et al. (2003). PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Communications in Mass Spectrometry, 17(20), 2337–2342.
    • (2003) Rapid Communications in Mass Spectrometry , vol.17 , Issue.20 , pp. 2337-2342
    • Ma, B.1    Zhang, K.2    Hendrie, C.3    Liang, C.4
  • 29
    • 70349125897 scopus 로고    scopus 로고
    • X-Rank: A robust algorithm for small molecule identification using tandem mass spectrometry
    • COI: 1:CAS:528:DC%2BD1MXhtVensrbO, PID: 19702277
    • Mylonas, R., Mauron, Y., Masselot, A., et al. (2009). X-Rank: A robust algorithm for small molecule identification using tandem mass spectrometry. Analytical Chemistry, 81(18), 7604–7610.
    • (2009) Analytical Chemistry , vol.81 , Issue.18 , pp. 7604-7610
    • Mylonas, R.1    Mauron, Y.2    Masselot, A.3
  • 30
    • 65649115837 scopus 로고    scopus 로고
    • On the inter-instrument and the inter-laboratory transferability of a tandem mass spectral reference library: 2. Optimization and characterization of the search algorithm
    • Oberacher, H., Pavlic, M., Libiseller, K., et al. (2009). On the inter-instrument and the inter-laboratory transferability of a tandem mass spectral reference library: 2. Optimization and characterization of the search algorithm. Journal of Mass Spectrometry (JMS), 44(4), 494–502.
    • (2009) Journal of Mass Spectrometry (JMS) , vol.44 , Issue.4 , pp. 494-502
    • Oberacher, H.1    Pavlic, M.2    Libiseller, K.3
  • 31
    • 21844457685 scopus 로고    scopus 로고
    • Fragmentation pathways of protonated peptides
    • COI: 1:CAS:528:DC%2BD2MXlvFShsLg%3D, PID: 15389847
    • Paizs, B., & Suhai, S. (2005). Fragmentation pathways of protonated peptides. Mass Spectrometry Reviews, 24(4), 508–548.
    • (2005) Mass Spectrometry Reviews , vol.24 , Issue.4 , pp. 508-548
    • Paizs, B.1    Suhai, S.2
  • 32
    • 0842285056 scopus 로고
    • The interpretation of collision-induced dissociation tandem mass spectra of peptides
    • COI: 1:CAS:528:DyaK28Xis1ShsQ%3D%3D
    • Papayannopoulos, I. (1995). The interpretation of collision-induced dissociation tandem mass spectra of peptides. Mass Spectrometry Reviews, 14(April), 49–73.
    • (1995) Mass Spectrometry Reviews , vol.14 , Issue.April , pp. 49-73
    • Papayannopoulos, I.1
  • 33
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • COI: 1:CAS:528:DC%2BD3cXhtF2ntw%3D%3D, PID: 10612281
    • Perkins, D. N., Pappin, D. J. C., Creasy, D. M., & Cottrell, J. S. (1999). Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20, 3551–3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 34
    • 84877343392 scopus 로고    scopus 로고
    • Computational mass spectrometry for small molecules
    • COI: 1:CAS:528:DC%2BC3sXot1Wmu70%3D, PID: 23453222
    • Scheubert, K., Hufsky, F., & Böcker, S. (2013). Computational mass spectrometry for small molecules. Journal of Cheminformatics, 5(1), 12.
    • (2013) Journal of Cheminformatics , vol.5 , Issue.1 , pp. 12
    • Scheubert, K.1    Hufsky, F.2    Böcker, S.3
  • 35
    • 32444432587 scopus 로고    scopus 로고
    • METLIN: A metabolite mass spectral database
    • COI: 1:CAS:528:DC%2BD2MXhtlSrtr%2FO, PID: 16404815
    • Smith, C. A., O’Maille, G., Want, E. J., et al. (2005). METLIN: A metabolite mass spectral database. Therapeutic Drug Monitoring, 27(6), 747–751.
    • (2005) Therapeutic Drug Monitoring , vol.27 , Issue.6 , pp. 747-751
    • Smith, C.A.1    O’Maille, G.2    Want, E.J.3
  • 36
    • 0000881748 scopus 로고
    • Optimization and testing of mass spectral library search algorithms for compound identification
    • COI: 1:CAS:528:DyaK2MXhtFGhsLk%3D, PID: 24222034
    • Stein, S. E., & Scott, D. R. (1994). Optimization and testing of mass spectral library search algorithms for compound identification. Journal of the American Society for Mass Spectrometry, 5(9), 859–866.
    • (1994) Journal of the American Society for Mass Spectrometry , vol.5 , Issue.9 , pp. 859-866
    • Stein, S.E.1    Scott, D.R.2
  • 37
    • 34748888866 scopus 로고    scopus 로고
    • Proposed minimum reporting standards for chemical analysis
    • COI: 1:CAS:528:DC%2BD2sXhtFOntbvL, PID: 24039616
    • Sumner, L. W., Amberg, A., Barrett, D., et al. (2007). Proposed minimum reporting standards for chemical analysis. Metabolomics, 3, 211–221.
    • (2007) Metabolomics , vol.3 , pp. 211-221
    • Sumner, L.W.1    Amberg, A.2    Barrett, D.3
  • 38
    • 84866123900 scopus 로고    scopus 로고
    • An accelerated workflow for untargeted metabolomics using the METLIN database
    • COI: 1:CAS:528:DC%2BC38XhtlamtbnJ, PID: 22965049
    • Tautenhahn, R., Cho, K., Uritboonthai, W., et al. (2012). An accelerated workflow for untargeted metabolomics using the METLIN database. Nature Biotechnology, 30(9), 826–828.
    • (2012) Nature Biotechnology , vol.30 , Issue.9 , pp. 826-828
    • Tautenhahn, R.1    Cho, K.2    Uritboonthai, W.3
  • 39
    • 80051682403 scopus 로고    scopus 로고
    • Advances in metabolite identification
    • COI: 1:CAS:528:DC%2BC3MXhtVSnsrzM, PID: 21827274
    • Wishart, D. S. (2011). Advances in metabolite identification. Bioanalysis, 3(15), 1769–1782.
    • (2011) Bioanalysis , vol.3 , Issue.15 , pp. 1769-1782
    • Wishart, D.S.1
  • 40
    • 58149202163 scopus 로고    scopus 로고
    • HMDB: A knowledgebase for the human metabolome
    • COI: 1:CAS:528:DC%2BD1cXhsFejt7fO, PID: 18953024
    • Wishart, D. S., Knox, C., Guo, A. C., et al. (2009). HMDB: A knowledgebase for the human metabolome. Nucleic Acids Research, 37, D603–D610.
    • (2009) Nucleic Acids Research , vol.37 , pp. D603-D610
    • Wishart, D.S.1    Knox, C.2    Guo, A.C.3
  • 41
    • 84876148784 scopus 로고    scopus 로고
    • HMDB 3.0: The Human Metabolome Database in 2013
    • COI: 1:CAS:528:DC%2BC38XhvV2ktrnP, PID: 23161693
    • Wishart, D. S., Jewison, T., Guo, A. C., et al. (2013). HMDB 3.0: The Human Metabolome Database in 2013. Nucleic Acids Research, 41, D801–D807.
    • (2013) Nucleic Acids Research , vol.41 , pp. D801-D807
    • Wishart, D.S.1    Jewison, T.2    Guo, A.C.3
  • 42
    • 77952302069 scopus 로고    scopus 로고
    • In silico fragmentation for computer assisted identification of metabolite mass spectra
    • PID: 20307295
    • Wolf, S., Schmidt, S., Müller-Hannemann, M., & Neumann, S. (2010). In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics, 11, 148.
    • (2010) BMC Bioinformatics , vol.11 , pp. 148
    • Wolf, S.1    Schmidt, S.2    Müller-Hannemann, M.3    Neumann, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.