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Volumn 53, Issue , 2014, Pages 41-48

Computational mass spectrometry for small-molecule fragmentation

Author keywords

Combinatorial fragmentation; Compound classification; Computational mass spectrometry; Computational method; Fragmentation tree; Library searching; Mass spectrometry (MS); Rule based prediction; Small molecule fragmentation; Small molecule identification

Indexed keywords

COMPUTATIONAL METHODS; MASS SPECTROMETRY;

EID: 84888191935     PISSN: 01659936     EISSN: 18793142     Source Type: Journal    
DOI: 10.1016/j.trac.2013.09.008     Document Type: Review
Times cited : (93)

References (53)
  • 1
    • 84858790233 scopus 로고    scopus 로고
    • 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.
    • (2012) Nat. Rev. Mol. Cell Biol. , vol.13 , pp. 263-269
    • Patti, G.J.1    Yanes, O.2    Siuzdak, G.3
  • 2
    • 84856575688 scopus 로고    scopus 로고
    • Metabolite identification and quantitation in LC-MS/MS-based metabolomics
    • Xiao J.F., Zhou B., Ressom H.W. Metabolite identification and quantitation in LC-MS/MS-based metabolomics. Trends Anal. Chem. 2012, 32:1-14.
    • (2012) Trends Anal. Chem. , vol.32 , pp. 1-14
    • Xiao, J.F.1    Zhou, B.2    Ressom, H.W.3
  • 3
    • 41049100247 scopus 로고    scopus 로고
    • Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry
    • Fiehn O. Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry. Trends Anal. Chem. 2008, 27:261-269.
    • (2008) Trends Anal. Chem. , vol.27 , pp. 261-269
    • Fiehn, O.1
  • 4
    • 78650173423 scopus 로고    scopus 로고
    • Computational mass spectrometry for metabolomics - a review
    • Neumann S., Böcker S. Computational mass spectrometry for metabolomics - a review. Anal. Bioanal. Chem. 2010, 398:2779-2788.
    • (2010) Anal. Bioanal. Chem. , vol.398 , pp. 2779-2788
    • Neumann, S.1    Böcker, S.2
  • 5
    • 78650737804 scopus 로고    scopus 로고
    • Advances in structure elucidation of small molecules using mass spectrometry
    • Kind T., Fiehn O. Advances in structure elucidation of small molecules using mass spectrometry. Bioanal. Rev. 2010, 2:23-60.
    • (2010) Bioanal. Rev. , vol.2 , pp. 23-60
    • Kind, T.1    Fiehn, O.2
  • 6
    • 84877343392 scopus 로고    scopus 로고
    • Computational mass spectrometry for small molecules
    • Scheubert K., Hufsky F., Böcker S. Computational mass spectrometry for small molecules. J. Cheminform. 2013, 5:12.
    • (2013) J. Cheminform. , vol.5 , pp. 12
    • Scheubert, K.1    Hufsky, F.2    Böcker, S.3
  • 7
    • 0000881748 scopus 로고
    • 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.
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 859-866
    • Stein, S.E.1    Scott, D.R.2
  • 8
    • 79960378447 scopus 로고    scopus 로고
    • Wavelet-and Fourier-transform-based spectrum similarity approaches to compound identification in gas chromatography/mass spectrometry
    • Koo I., Zhang X., Kim S. Wavelet-and Fourier-transform-based spectrum similarity approaches to compound identification in gas chromatography/mass spectrometry. Anal. Chem. 2011, 83:5631-5638.
    • (2011) Anal. Chem. , vol.83 , pp. 5631-5638
    • Koo, I.1    Zhang, X.2    Kim, S.3
  • 9
    • 84859746023 scopus 로고    scopus 로고
    • A method of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry
    • Kim S., Koo I., Wei X., Zhang X. A method of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry. Bioinformatics 2012, 28:1158-1163.
    • (2012) Bioinformatics , vol.28 , pp. 1158-1163
    • Kim, S.1    Koo, I.2    Wei, X.3    Zhang, X.4
  • 10
    • 84865769818 scopus 로고    scopus 로고
    • Mass spectral reference libraries: an ever-expanding resource for chemical identification
    • Stein S.E. Mass spectral reference libraries: an ever-expanding resource for chemical identification. Anal. Chem. 2012, 84:7274-7282.
    • (2012) Anal. Chem. , vol.84 , pp. 7274-7282
    • Stein, S.E.1
  • 11
    • 0000355793 scopus 로고
    • Estimating probabilities of correct identification from results of mass spectral library searches
    • Stein S.E. Estimating probabilities of correct identification from results of mass spectral library searches. J. Am. Soc. Mass Spectrom. 1994, 5:316-323.
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 316-323
    • Stein, S.E.1
  • 12
    • 80053600914 scopus 로고    scopus 로고
    • An empirical bayes model using a competition score for metabolite identification in gas chromatography mass spectrometry
    • Jeong J., Shi X., Zhang X., Kim S., Shen C. An empirical bayes model using a competition score for metabolite identification in gas chromatography mass spectrometry. BMC Bioinf. 2011, 12:392.
    • (2011) BMC Bioinf. , vol.12 , pp. 392
    • Jeong, J.1    Shi, X.2    Zhang, X.3    Kim, S.4    Shen, C.5
  • 13
    • 3042521543 scopus 로고    scopus 로고
    • Spectral similarity versus structural similarity: mass spectrometry
    • Demuth W., Karlovits M., Varmuza K. Spectral similarity versus structural similarity: mass spectrometry. Anal. Chim. Acta 2004, 516:75-85.
    • (2004) Anal. Chim. Acta , vol.516 , pp. 75-85
    • Demuth, W.1    Karlovits, M.2    Varmuza, K.3
  • 14
    • 79953273023 scopus 로고    scopus 로고
    • Evaluation of the comparability of spectra generated using a tuning point protocol on twelve electrospray ionisation tandem-in-space mass spectrometers
    • Champarnaud E., Hopley C. Evaluation of the comparability of spectra generated using a tuning point protocol on twelve electrospray ionisation tandem-in-space mass spectrometers. Rapid Commun. Mass Spectrom. 2011, 25:1001-1007.
    • (2011) Rapid Commun. Mass Spectrom. , vol.25 , pp. 1001-1007
    • Champarnaud, E.1    Hopley, C.2
  • 15
    • 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., Schubert B., Sulyok M., Schuhmacher R., Csaszar E., Köfeler H.C. On the inter-instrument and the inter-laboratory transferability of a tandem mass spectral reference library: 2. Optimization and characterization of the search algorithm. J. Mass Spectrom. 2009, 44:494-502.
    • (2009) J. Mass Spectrom. , vol.44 , pp. 494-502
    • Oberacher, H.1    Pavlic, M.2    Libiseller, K.3    Schubert, B.4    Sulyok, M.5    Schuhmacher, R.6    Csaszar, E.7    Köfeler, H.C.8
  • 16
    • 84890858010 scopus 로고    scopus 로고
    • Maximizing MS/MS Fragmentation in the Ion Trap Using CID Voltage Ramping, Technical Report 5988-0704EN, Agilent Technologies
    • P. Goodley, Maximizing MS/MS Fragmentation in the Ion Trap Using CID Voltage Ramping, Technical Report 5988-0704EN, Agilent Technologies, 2007.
    • (2007)
    • Goodley, P.1
  • 17
    • 46749093781 scopus 로고    scopus 로고
    • Towards a universal product ion mass spectral library - reproducibility of product ion spectra across eleven different mass spectrometers
    • Hopley C., Bristow T., Lubben A., Simpson A., Bull E., Klagkou K., Herniman J., Langley J. Towards a universal product ion mass spectral library - reproducibility of product ion spectra across eleven different mass spectrometers. Rapid Commun. Mass Spectrom. 2008, 22:1779-1786.
    • (2008) Rapid Commun. Mass Spectrom. , vol.22 , pp. 1779-1786
    • Hopley, C.1    Bristow, T.2    Lubben, A.3    Simpson, A.4    Bull, E.5    Klagkou, K.6    Herniman, J.7    Langley, J.8
  • 19
    • 15744370949 scopus 로고    scopus 로고
    • New strategy of mass spectrum simulation based on reduced and concentrated knowledge databases
    • Fan B., Chen H., Petitjean M., Panaye A., Doucet J.-P., Xia H., Yuan S. New strategy of mass spectrum simulation based on reduced and concentrated knowledge databases. Spectrosc. Lett. 2005, 38:145-170.
    • (2005) Spectrosc. Lett. , vol.38 , pp. 145-170
    • Fan, B.1    Chen, H.2    Petitjean, M.3    Panaye, A.4    Doucet, J.-P.5    Xia, H.6    Yuan, S.7
  • 20
    • 1642506499 scopus 로고
    • Topological mapping of organic molecules
    • Lederberg J. Topological mapping of organic molecules. Proc. Natl. Acad. Sci. USA 1965, 53:134-139.
    • (1965) Proc. Natl. Acad. Sci. USA , vol.53 , pp. 134-139
    • Lederberg, J.1
  • 21
    • 84885596926 scopus 로고
    • How DENDRAL was conceived and born, in: ACM Conf. on the History of Medical Informatics, History of Medical Informatics Archive
    • J. Lederberg, How DENDRAL was conceived and born, in: ACM Conf. on the History of Medical Informatics, History of Medical Informatics Archive, 1987, pp. 5-19. http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.185.2510.
    • (1987) , pp. 5-19
    • Lederberg, J.1
  • 22
    • 33646747122 scopus 로고    scopus 로고
    • MOLGEN-MS: evaluation of low resolution electron impact mass spectra with MS classification and exhaustive structure generation
    • Kerber A., Laue R., Meringer M., Varmuza K. MOLGEN-MS: evaluation of low resolution electron impact mass spectra with MS classification and exhaustive structure generation. Adv. Mass Spectrom. 2001, 15:939-940.
    • (2001) Adv. Mass Spectrom. , vol.15 , pp. 939-940
    • Kerber, A.1    Laue, R.2    Meringer, M.3    Varmuza, K.4
  • 23
    • 33846435744 scopus 로고    scopus 로고
    • CASE via MS: ranking structure candidates by mass spectra
    • Kerber A., Meringer M., Rücker C. CASE via MS: ranking structure candidates by mass spectra. Croat. Chem. Acta 2006, 79:449-464.
    • (2006) Croat. Chem. Acta , vol.79 , pp. 449-464
    • Kerber, A.1    Meringer, M.2    Rücker, C.3
  • 24
    • 48749115768 scopus 로고    scopus 로고
    • Mass spectrometry for the identification of the discriminating signals from metabolomics: current status and future trends
    • Werner E., Heilier J.-F., Ducruix C., Ezan E., Junot C., Tabet J.-C. Mass spectrometry for the identification of the discriminating signals from metabolomics: current status and future trends. J. Chromatogr. B 2008, 871:143-163.
    • (2008) J. Chromatogr. B , vol.871 , pp. 143-163
    • Werner, E.1    Heilier, J.-F.2    Ducruix, C.3    Ezan, E.4    Junot, C.5    Tabet, J.-C.6
  • 25
    • 49049121462 scopus 로고    scopus 로고
    • Mass spectral metabonomics beyond elemental formula: chemical database querying by matching experimental with computational fragmentation spectra
    • Hill D.W., Kertesz T.M., Fontaine D., Friedman R., Grant D.F. Mass spectral metabonomics beyond elemental formula: chemical database querying by matching experimental with computational fragmentation spectra. Anal. Chem. 2008, 80:5574-5582.
    • (2008) Anal. Chem. , vol.80 , pp. 5574-5582
    • Hill, D.W.1    Kertesz, T.M.2    Fontaine, D.3    Friedman, R.4    Grant, D.F.5
  • 26
    • 66149115595 scopus 로고    scopus 로고
    • Matching structures to mass spectra using fragmentation patterns: are the results as good as they look?
    • Schymanski E.L., Meringer M., Brack W. Matching structures to mass spectra using fragmentation patterns: are the results as good as they look?. Anal. Chem. 2009, 81:3608-3617.
    • (2009) Anal. Chem. , vol.81 , pp. 3608-3617
    • Schymanski, E.L.1    Meringer, M.2    Brack, W.3
  • 27
    • 79960981890 scopus 로고    scopus 로고
    • Applying in-silico retention index and mass spectra matching for identification of unknown metabolites in accurate mass GC-TOF mass spectrometry
    • Kumari S., Stevens D., Kind T., Denkert C., Fiehn O. Applying in-silico retention index and mass spectra matching for identification of unknown metabolites in accurate mass GC-TOF mass spectrometry. Anal. Chem. 2011, 83:5895-5902.
    • (2011) Anal. Chem. , vol.83 , pp. 5895-5902
    • Kumari, S.1    Stevens, D.2    Kind, T.3    Denkert, C.4    Fiehn, O.5
  • 29
    • 27544443321 scopus 로고    scopus 로고
    • Automated assignment of high-resolution collisionally activated dissociation mass spectra using a systematic bond disconnection approach
    • Hill A.W., Mortishire-Smith R.J. Automated assignment of high-resolution collisionally activated dissociation mass spectra using a systematic bond disconnection approach. Rapid Commun. Mass Spectrom. 2005, 19:3111-3118.
    • (2005) Rapid Commun. Mass Spectrom. , vol.19 , pp. 3111-3118
    • Hill, A.W.1    Mortishire-Smith, R.J.2
  • 31
    • 77952302069 scopus 로고    scopus 로고
    • In silico fragmentation for computer assisted identification of metabolite mass spectra
    • Wolf S., Schmidt S., Müller-Hannemann M., Neumann S. In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinf. 2010, 11:148.
    • (2010) BMC Bioinf. , vol.11 , pp. 148
    • Wolf, S.1    Schmidt, S.2    Müller-Hannemann, M.3    Neumann, S.4
  • 33
    • 84875154340 scopus 로고    scopus 로고
    • MetFusion: integration of compound identification strategies
    • Gerlich M., Neumann S. MetFusion: integration of compound identification strategies. J. Mass Spectrom. 2013, 48:291-298.
    • (2013) J. Mass Spectrom. , vol.48 , pp. 291-298
    • Gerlich, M.1    Neumann, S.2
  • 34
    • 0142104153 scopus 로고    scopus 로고
    • Small molecules as mathematical partitions
    • Sweeney D.L. Small molecules as mathematical partitions. Anal. Chem. 2003, 75:5362-5373.
    • (2003) Anal. Chem. , vol.75 , pp. 5362-5373
    • Sweeney, D.L.1
  • 35
    • 0001144659 scopus 로고    scopus 로고
    • Mass spectral classifiers for supporting systematic structure elucidation
    • Varmuza K., Werther W. Mass spectral classifiers for supporting systematic structure elucidation. J. Chem. Inf. Comput. Sci. 1996, 36:323-333.
    • (1996) J. Chem. Inf. Comput. Sci. , vol.36 , pp. 323-333
    • Varmuza, K.1    Werther, W.2
  • 36
    • 84866437252 scopus 로고    scopus 로고
    • Metabolite identification and molecular fingerprint prediction via machine learning
    • Proc. of European Conference on Computational Biology (ECCB 2012).
    • M. Heinonen, H. Shen, N. Zamboni, J. Rousu, Metabolite identification and molecular fingerprint prediction via machine learning, Bioinformatics 28 (2012) 2333-2341. Proc. of European Conference on Computational Biology (ECCB 2012).
    • (2012) Bioinformatics , vol.28 , pp. 2333-2341
    • Heinonen, M.1    Shen, H.2    Zamboni, N.3    Rousu, J.4
  • 38
    • 0000082285 scopus 로고
    • Computer-aided interpretation of mass spectra. III. Self-training interpretive and retrieval system
    • Kwok K.-S., Venkataraghavan R., McLafferty F.W. Computer-aided interpretation of mass spectra. III. Self-training interpretive and retrieval system. J. Am. Chem. Soc. 1973, 95:4185-4194.
    • (1973) J. Am. Chem. Soc. , vol.95 , pp. 4185-4194
    • Kwok, K.-S.1    Venkataraghavan, R.2    McLafferty, F.W.3
  • 39
    • 0026621958 scopus 로고
    • Rapid and accurate method for estimating molecular weights of organic compounds from low resolution mass spectra
    • Scott D.R. Rapid and accurate method for estimating molecular weights of organic compounds from low resolution mass spectra. Chemom. Intell. Lab. 1992, 16:193-202.
    • (1992) Chemom. Intell. Lab. , vol.16 , pp. 193-202
    • Scott, D.R.1
  • 40
    • 0026628623 scopus 로고
    • Pattern recognition/expert system for mass spectra of volatile toxic and other organic compounds
    • Scott D.R. Pattern recognition/expert system for mass spectra of volatile toxic and other organic compounds. Anal. Chim. Acta 1992, 265:43-54.
    • (1992) Anal. Chim. Acta , vol.265 , pp. 43-54
    • Scott, D.R.1
  • 41
    • 0027233454 scopus 로고
    • Large scale evaluation of a pattern recognition/expert system for mass spectral molecular weight estimation
    • Scott D.R., Levitsky A., Stein S.E. Large scale evaluation of a pattern recognition/expert system for mass spectral molecular weight estimation. Anal. Chim. Acta 1993, 278:137-147.
    • (1993) Anal. Chim. Acta , vol.278 , pp. 137-147
    • Scott, D.R.1    Levitsky, A.2    Stein, S.E.3
  • 42
    • 79954566035 scopus 로고    scopus 로고
    • 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.
    • (2010) Metabolomics , vol.6 , pp. 322-333
    • Hummel, J.1    Strehmel, N.2    Selbig, J.3    Walther, D.4    Kopka, J.5
  • 43
    • 58349086772 scopus 로고    scopus 로고
    • SIRIUS: decomposing isotope patterns for metabolite identification
    • Böcker S., Letzel M., Liptak Z.S., Pervukhin A. SIRIUS: decomposing isotope patterns for metabolite identification. Bioinformatics 2009, 25:218-224.
    • (2009) Bioinformatics , vol.25 , pp. 218-224
    • Böcker, S.1    Letzel, M.2    Liptak, Z.S.3    Pervukhin, A.4
  • 44
    • 49549101405 scopus 로고    scopus 로고
    • Towards de novo identification of metabolites by analyzing tandem mass spectra
    • Proc. of European Conference on Computational Biology (ECCB 2008).
    • S. Böcker, F. Rasche, Towards de novo identification of metabolites by analyzing tandem mass spectra, Bioinformatics 24 (2008) I49-I55. Proc. of European Conference on Computational Biology (ECCB 2008).
    • (2008) Bioinformatics , vol.24
    • Böcker, S.1    Rasche, F.2
  • 46
    • 84864025665 scopus 로고    scopus 로고
    • De novöanalysis of electron impact mass spectra using fragmentation trees
    • Hufsky F., Rempt M., Rasche F., Pohnert G., Böcker S. De novöanalysis of electron impact mass spectra using fragmentation trees. Anal. Chim. Acta 2012, 739:67-76.
    • (2012) Anal. Chim. Acta , vol.739 , pp. 67-76
    • Hufsky, F.1    Rempt, M.2    Rasche, F.3    Pohnert, G.4    Böcker, S.5
  • 50
    • 60649112635 scopus 로고    scopus 로고
    • Determination of ion structures in structurally related compounds using precursor ion fingerprinting
    • Sheldon M.T., Mistrik R., Croley T.R. Determination of ion structures in structurally related compounds using precursor ion fingerprinting. J. Am. Soc. Mass Spectrom. 2009, 20:370-376.
    • (2009) J. Am. Soc. Mass Spectrom. , vol.20 , pp. 370-376
    • Sheldon, M.T.1    Mistrik, R.2    Croley, T.R.3
  • 53
    • 80955139621 scopus 로고    scopus 로고
    • Computing fragmentation trees from metabolite multiple mass spectrometry data
    • Scheubert K., Hufsky F., Rasche F., Böcker S. Computing fragmentation trees from metabolite multiple mass spectrometry data. J. Comput. Biol. 2011, 18:1383-1397.
    • (2011) J. Comput. Biol. , vol.18 , pp. 1383-1397
    • Scheubert, K.1    Hufsky, F.2    Rasche, F.3    Böcker, S.4


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