Correction of precursor and product ion relative abundances in order to standardize CID spectra and improve Ecom50 accuracy for non-targeted metabolomics

Metabolomics

Volumn 11, Issue 3, 2015, Pages 753-763

  Dubey, Ritvik ^a   Hill, Dennis W ^a   Lai, Steven ^b   Chen, Ming Hui ^a   Grant, David F ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

^b WATERS CORPORATION   (United States)

Author keywords

CID spectrum; Ecom50; RF voltage; RF only ion guides; Untargeted metabolomics

Indexed keywords

8 QUINOLINOL; ANILINE; BENZIMIDAZOLE; FORMAMIDE; GLYCINE; HELIUM; IMIDAZOLE; NITROGEN; PACLITAXEL; RESERPINE; STRYCHNINE; TRIFLUOROACETIC ACID;

ARTICLE; CHEMICAL BOND; COLLISIONALLY ACTIVATED DISSOCIATION; ELECTRIC POTENTIAL; ENERGY; ION TRANSPORT; KINETICS; MASS SPECTROMETRY; METABOLOMICS; PRECURSOR; SPECTROMETRY;

EID: 84929459089     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-014-0732-0     Document Type: Article

References (27)

1. Berendsen, B. A., Stolker, L. M., & Nielen, M. F. (2013). The (Un)certainty of selectivity in liquid chromatography tandem mass spectrometry. Journal of the American Society for Mass Spectrometry,24(1), 154–163. doi:10.1007/s13361-012-0501-0.
2. Commisso, M., Strazzer, P., Toffali, K., Stocchero, M., & Guzzo, F. (2013). Untargeted metabolomics: An emerging approach to determine the composition of herbal products. Computational and Structural Biotechnology Journal; 2013: Volume 4. Retrieved from http://journals.sfu.ca/rncsb/index.php/csbj/article/view/csbj.201301007/219.
3. Creek, D. J., Jankevics, A., Burgess, K. E. V., Breitling, R., & Barrett, M. P. (2012). IDEOM: An excel interface for analysis of LC–MS-based metabolomics data. Bioinformatics,28(7), 1048–1049. doi:10.1093/bioinformatics/bts069.
4. Dettmer, K., Aronov, P. A., & Hammock, B. D. (2007). Mass spectrometry-based metabolomics. Mass Spectrometry Reviews,26(1), 51–78. doi:10.1002/mas.20108.
5. Douglas, D. J., & French, J. B. (1992). Collisional focusing effects in radio frequency quadrupoles. Journal of the American Society for Mass Spectrometry,3(4), 398–408. doi:10.1016/1044-0305(92)87067-9.
6. Dunn, O. J. (1961). Multiple comparisons among means. Journal of the American Statistical Association,56(293), 52–64. doi:10.1080/01621459.1961.10482090.
7. Dunn, W., Erban, A., Weber, R. M., Creek, D., Brown, M., Breitling, R., et al. (2013). Mass appeal: Metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics,9(1), 44–66. doi:10.1007/s11306-012-0434-4.
8. Gerlich, D. (1992). Inhomogeneous RF fields: A versatile tool for the study of processes with slow ions. Advances in Chemical Physics, 82, 1–176. doi:10.1002/9780470141397.ch1.
9. Giles, K., Pringle, S. D., Worthington, K. R., Little, D., Wildgoose, J. L., & Bateman, R. H. (2004). Applications of a travelling wave-based radio-frequency-only stacked ring ion guide. Rapid Communications in Mass Spectrometry,18(20), 2401–2414. doi:10.1002/rcm.1641.
10. Guilhaus, M. (1994). Spontaneous and deflected drift-trajectories in orthogonal acceleration time-of-flight mass spectrometry. Journal of the American Society for Mass Spectrometry,5(6), 588–595. doi:10.1016/1044-0305(94)90009-4.
11. Guzowski, J. P, Jr, & Hieftje, G. M. (2001a). Characteristics of a rf-only hexapole ion-guide interface for plasma-source time-of-flight mass spectrometry. Journal of Analytical Atomic Spectrometry,16(8), 781–792. doi:10.1039/B004381H.
12. Guzowski, J. P, Jr., & Hieftje, G. M. (2001b). Characteristics of a rf-only hexapole ion-guide interface for plasma-source time-of-flight mass spectrometry. Journal of Analytical Atomic Spectrometry,16(8), 781–792. doi:10.1039/b004381h.
13. 50 and retention index models for nontargeted metabolomics: Identification of 1,3-dicyclohexylurea in human serum by HPLC/mass spectrometry. Journal of Chemical Information and Modeling,52(5), 1222–1237. doi:10.1021/ci300092s.
14. Hamdalla, M. A., Mandoiu, I. I., Hill, D. W., Rajasekaran, S., & Grant, D. F. (2013). BioSM: Metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space. Journal of Chemical Information and Modeling,53(3), 601–612. doi:10.1021/ci300512q.
15. 50 values between mass spectrometers: Effect of collision cell radiofrequency voltage on calculated survival yield. Rapid communications in mass spectrometry: RCM,26(19), 2303–2310. doi:10.1002/rcm.6353.
16. Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., et al. (2010). MassBank: A public repository for sharing mass spectral data for life sciences. Journal of Mass Spectrometry,45(7), 703–714. doi:10.1002/jms.1777.
17. Kaddurah-Daouk, R., Kristal, B. S., & Weinshilboum, R. M. (2008). Metabolomics: A global biochemical approach to drug response and disease. Annual Review of Pharmacology and Toxicology,48(1), 653–683. doi:10.1146/annurev.pharmtox.48.113006.094715.
18. Knyazev, V., & Stein, S. (2010). Classical trajectories and RRKM modeling of collisional excitation and dissociation of benzylammonium and tert-butyl benzylammonium ions in a quadrupole-hexapole-quadrupole tandem mass spectrometer. Journal of the American Society for Mass Spectrometry,21(3), 425–439. doi:10.1016/j.jasms.2009.11.007.
19. Milne, S. B., Mathews, T. P., Myers, D. S., Ivanova, P. T., & Brown, H. A. (2013). Sum of the parts: Mass spectrometry-based metabolomics. Biochemistry,52(22), 3829–3840. doi:10.1021/bi400060e.
20. Szabo, I. (1986). New ion-optical devices utilizing oscillatory electric fields I. Principle of operation and analytical theory of multipole devices with two-dimensional electric fields. International Journal of Mass Spectrometry and Ion Processes,73(3), 197–235. doi:10.1016/0168-1176(86)80001-5.
21. Tanner, S. D., & Baranov, V. I. (1999). A dynamic reaction cell for inductively coupled plasma mass spectrometry (ICP-DRC-MS) II. Reduction of interferences produced within the cell. Journal of the American Society for Mass Spectrometry,10(11), 1083–1094. doi:10.1016/S1044-0305(99)00081-1.
22. Tautenhahn, R., Cho, K., Uritboonthai, W., Zhu, Z., Patti, G. J., & Siuzdak, G. (2012). An accelerated workflow for untargeted metabolomics using the METLIN database. Nature biotechnology, 30(9), 826–828. Retrieved from http://europepmc.org/abstract/MED/22965049.
23. Thomson, B. A., Douglas, D. J., Corr, J. J., Hager, J. W., & Jolliffe, C. L. (1995). Improved collisionally activated dissociation efficiency and mass resolution on a triple quadrupole mass spectrometer system. Analytical Chemistry,67(10), 1696–1704. doi:10.1021/ac00106a008.
24. Vékey, K. (1996). Internal energy effects in mass spectrometry. Journal of Mass Spectrometry,31(5), 445–463. doi:10.1002/(SICI)1096-9888(199605)31:5<445:AID-JMS354>3.0.CO;2-G.
25. Vinayavekhin, N., & Saghatelian, A. (2001). Untargeted Metabolomics. Hoboken, NJ: John Wiley & Sons, Inc. doi:10.1002/0471142727.mb3001s90.
26. Wishart, D. S., Knox, C., Guo, A. C., Eisner, R., Young, N., Gautam, B., et al. (2009). HMDB: A knowledgebase for the human metabolome. Nucleic Acids Research,37(suppl 1), D603–D610. doi:10.1093/nar/gkn810.
27. Zimmer, J. O., P. W., & M. (1997). New results on the absolute ion detection efficiencies of a microchannel plate. Measurement Science and Technology, 8(4), 351. Retrieved from http://stacks.iop.org/0957-0233/8/i=4/a=001.