A new strategy for MS/MS data acquisition applying multiple data dependent experiments on Orbitrap mass spectrometers in non-targeted metabolomic applications
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- 作者：Graham Mullard ; James W. Allwood ; Ralf Weber ; Marie Brown ; Paul Begley…
- 关键词：Metabolite annotation ; Metabolite identification ; MS/MS ; CID ; HCD ; Orbitrap
- 刊名：Metabolomics
- 出版年：2015
- 出版时间：October 2015
- 年：2015
- 卷：11
- 期：5
- 页码：1068-1080
- 全文大小：1,069 KB
- 参考文献：Bird, S. S., Marur, V. R., Sniatynski, M. J., Greenberg, H. K., & Kristal, B. S. (2011). Serum lipidomics profiling using LC-MS and high-energy collisional dissociation fragmentation: Focus on triglyceride detection and characterization. Analytical Chemistry, 83, 6648-657.PubMed Central CrossRef PubMed
Brown, M., Wedge, D. C., Goodacre, R., et al. (2011). Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets. Bioinformatics, 27, 1108-112.PubMed Central CrossRef PubMed
Bushee, J. L., & Argikar, U. A. (2010). An experimental approach to enhance precursor ion fragmentation for metabolite identification studies: Application of dual collision cells in an orbital trap. Rapid Communications in Mass Spectrometry, 25, 1356-362.CrossRef
Calderón-Santiago, M., Priego-Capote, F., & Luque de Castro, M. D. (2014). Enhanced detection and identification in metabolomics by use of LC–MS/MS untargeted analysis in combination with gas-phase fractionation. Analytical Chemistry, 86, 7558-565.CrossRef PubMed
Creek, D. J., Jankevics, A., Breitling, R., Watson, D. G., Barrett, M. P., & Burgess, K. E. (2011). oward global metabolomics analysis with hydrophilic interaction liquid chromatography-mass spectrometry: Improved metabolite identification by retention time prediction. Analytical Chemistry, 83, 8703-710.CrossRef PubMed
Dunn, W. B., Broadhurst, D. I., Atherton, H. J., Goodacre, R., & Griffin, J. L. (2011a). Systems level studies of mammalian metabolomes: The roles of mass spectrometry and nuclear magnetic resonance spectroscopy. Chemical Society Reviews, 40, 387-26.CrossRef PubMed
Dunn, W. B., Broadhurst, D., Begley, P., et al. (2011b). Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nature Protocols, 6, 1060-083.CrossRef PubMed
Dunn, W. B., Erban, A., Weber, R. J. M., et al. (2013). Mass appeal: Metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics, 9(Suppl), 44-6.CrossRef
Dunn, W. B.; Lin, W.; Broadhurst, D. et al. (2014). Molecular phenotyping of a UK population: Defining the human serum metabolome. Metabolomics. doi:10.-007/?s11306-014-0707-1 .
Godfrey, A. R., Williams, C. M., Dudley, E., et al. (2009). Investigation of uremic analytes in hemodialysate and their structural elucidation from accurate mass maps generated by a multi-dimensional liquid chromatography/mass spectrometry approach. Rapid Communications in Mass Spectrometry, 23, 3194-204.CrossRef PubMed
Hall, L. M., Hall, L. H., Kertesz, T. M., et al. (2012). Development of Ecom50 and retention index models for nontargeted metabolomics: Identification of 1,3-dicyclohexylurea in human serum by HPLC/mass spectrometry. Chemical Information and Modeling, 52, 1222-237.CrossRef
Hoopmann, M. R., Merrihew, G. E., von Haller, P. D., & MacCoss, M. J. (2009). Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures. Journal of Proteome Research, 8, 1870-875.PubMed Central CrossRef PubMed
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, 703-14.CrossRef PubMed
Kalli, A., Smith, G. T., Sweredoski, M. J., & Hess, S. (2013). Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: Focus on LTQ-Orbitrap mass analyzers. Journal of Proteome Research, 12, 3071-086.PubMed Central CrossRef PubMed
Kind, T., & Fiehn, O. (2007). Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics, 8, 105.PubMed Central CrossRef PubMed
Kind, T., & Fiehn, O. (2010). Advances in structure elucidation of small molecules using mass spectrometry. Bioanalytical Reviews, 2, 23-0.PubMed Central CrossRef PubMed
Manna, S. K., Patterson, A. D., Yang, Q., et al. (2011). UPLC–MS-based urine metabolomics reveals indole-3-lactic acid and phenyllactic acid as conserved biomarkers for alcohol-induced liver disease in the Ppara-null mouse model. Journal of Proteome Research, 10, 4120-133.PubMed Central CrossRef PubMed
Neumann, S., Thum, A., & B?ttcher, C. (2013). Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data. Metabolomics, 9(suppl), S84–S91.CrossRef
Nicholson, J. K., Lindon, J. C., & Holmes, E. (1999). ‘Metabonomics- Understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica, 29, 1181-189.CrossRef PubMed
Olsen, J. V., Macek, B., Lange, O., Makarov, A., Horning, S., & Mann, M. (2007). Higher-energy C-trap dissociation for peptide modification analysis. Nature Methods, 4, 709-12.CrossRef PubMed
Plumb, R. S., Johnson, K. A., - 作者单位：Graham Mullard (1) (3)
James W. Allwood (4)
Ralf Weber (4)
Marie Brown (1) (3)
Paul Begley (1) (3)
Katherine A. Hollywood (1) (3)
Martin Jones (4)
Richard D. Unwin (1) (3)
Paul N. Bishop (1) (2) (3)
Garth J. S. Cooper (1) (3) (5) (6)
Warwick B. Dunn (1) (3) (4)
1. Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, M13 9WL, UK
3. Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, M13 9WL, UK
4. School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
2. Centre for Hearing and Vision Research, Institute of Human Development, Faculty of Medical and Human Sciences, The University of Manchester, Manchester, M13 9WL, UK
5. Maurice Wilkins Centre for Molecular Biodiscovery, Faculty of Science, University of Auckland, Auckland, 1020, New Zealand
6. Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK - 刊物主题：Biochemistry, general; Molecular Medicine; Cell Biology; Developmental Biology; Biomedicine general;
- 出版者：Springer US
- ISSN：1573-3890
文摘
The annotation and identification of metabolites is a current bottleneck in non-targeted metabolomics studies. Although accurate measurement of m/z is applied routinely in UPLC–MS applications to putatively annotate metabolites, the acquisition of MS/MS or MS n data is required to deduce structural information, further reducing the chemical search-space and providing greater confidence in metabolite annotation by comparison to mass spectral databases. Here we propose an innovative new strategy for data dependent acquisition (DDA) for on-line MS/MS data acquisition in parallel to full-scan metabolite profiling on LTQ-Orbitrap mass spectrometers. We recommend the application of different and integrated DDA MS/MS experiments to increase the coverage of unique metabolites for which MS/MS data were acquired. We demonstrate, for the first time, that the integrated application of both CID and higher-energy collisional dissociation ion activation methods, multiple different activation energies and narrow precursor ion m/z ranges of 100 or 300 for acquisition of MS/MS spectra provide complementary information and increases the number of unique metabolites for which MS/MS data is acquired. The strategies herein provide a different approach for data acquisition to increase the number of unique MS/MS mass spectra acquired for metabolite annotation purposes in non-targeted metabolomics studies. MS/MS data are available on request from the corresponding author. Keywords Metabolite annotation Metabolite identification MS/MS CID HCD Orbitrap