Metabolomics and lipidomics using traveling-wave ion mobility mass spectrometry

Nature Protocols

Volumn 12, Issue 4, 2017, Pages 797-813

  Paglia, Giuseppe ^a   Astarita, Giuseppe ^b  

^a University of Lubeck   (Italy)

^b GEORGETOWN UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIPID;

ARTICLE; BRAIN; CALIBRATION; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; DATA PROCESSING; DIFFERENTIAL MOBILITY SPECTROMETRY; DRIFT TIME ION MOBILITY SPECTROMETRY; FIELD ASYMMETRIC ION MOBILITY SPECTROMETRY; INTERMETHOD COMPARISON; ION MOBILITY SPECTROMETRY; LIPID ANALYSIS; LIPIDOMICS; LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY; METABOLITE; METABOLOMICS; PRIORITY JOURNAL; SIGNAL NOISE RATIO; TRAPPED ION MOBILITY SPECTROMETRY; TRAVELING WAVE ION MOBILITY SPECTROMETRY; LIPID METABOLISM; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PROCEDURES; TIME FACTOR;

CHROMATOGRAPHY, LIQUID; LIPID METABOLISM; MASS SPECTROMETRY; METABOLOMICS; TIME FACTORS;

EID: 85021309065     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2017.013     Document Type: Article

References (64)

1. Shah, V. et al. Enhanced data-independent analysis of lipids using ion mobility-TOFMS(E) to unravel quantitative and qualitative information in human plasma. Rapid Commun. Spectrom. 27, 2195-2200 (2013).
2. Hart, P.J., Francese, S., Claude, E., Woodroofe, M.N. & Clench, M.R. MALDI-MS imaging of lipids in ex vivo human skin. Anal. Bioanal. Chem. 401, 115-125 (2011).
3. Damen, C.W., Isaac, G., Langridge, J., Hankemeier, T. & Vreeken, R.J. Enhanced lipid isomer separation in human plasma using reversed-phase UPLC with ion-mobility/high-resolution MS detection. J. Lipid Res. 55, 1772-1783 (2014).
4. Kim, H.I. et al. Structural characterization of unsaturated phosphatidylcholines using traveling wave ion mobility spectrometry. Anal. Chem. 81, 8289-8297 (2009).
5. Castro-Perez, J. et al. Localization of fatty acyl and double bond positions in phosphatidylcholines using a dual stage CID fragmentation coupled with ion mobility mass spectrometry. J. Am. Soc. Mass Spectrom. 22, 1552-1567 (2011).
6. Kaur-Atwal, G. et al. Determination of testosterone and epitestosterone glucuronides in urine by ultra performance liquid chromatography-ion mobility-mass spectrometry. Analyst 136, 3911-3916 (2011).
7. Ahonen, L. et al. Separation of steroid isomers by ion mobility mass spectrometry. J. Chromatogr. A 1310, 133-137 (2013).
8. Dong, L. et al. Collision cross-section determination and tandem mass spectrometric analysis of isomeric carotenoids using electrospray ion mobility time-of-flight mass spectrometry. Anal. Chem. 82, 9014-9021 (2010).
9. Domalain, V. et al. Use of transition metals to improve the diastereomers differentiation by ion mobility and mass spectrometry. J. Mass Spectrom. 49, 423-427 (2014).
10. Malkar, A.D. et al. Metabolic profiling of human saliva before and after induced physiological stress by ultra-high performance liquid chromatography-ion mobility-mass spectrometry. Metabolomics 9, 1192-1201 (2013).
11. Dwivedi, P., Schultz, A.J. & Hill, H.H. Metabolic profiling of human blood by high resolution ion mobility mass spectrometry (IM-MS). Int. J. Mass Spectrom. 298, 78-90 (2010).
12. Dwivedi, P. et al. Metabolic profiling of Escherichia coli by ion mobility-mass spectrometry with MALDI ion source. J. Mass Spectrom. 45, 1383-1393 (2010).
13. Kaplan, K. et al. Monitoring dynamic changes in lymph metabolome of fasting and fed rats by electrospray ionization-ion mobility mass spectrometry (ESI-IMMS). Anal. Chem. 81, 7944-7953 (2009).
14. Harry, E.L., Weston, D.J., Bristow, A.W., Wilson, I.D. & Creaser, C.S. An approach to enhancing coverage of the urinary metabonome using liquid chromatography-ion mobility-mass spectrometry. J. Chromatogr B, Analyt. Technol. Biomed. Life Sci. 871, 357-361 (2008).
15. Lapthorn, C., Pullen, F. & Chowdhry, B.Z. Ion mobility spectrometry-mass spectrometry (IMS-MS) of small molecules: separating and assigning structures to ions. Mass Spectrom. Rev. 32, 43-71 (2013).
16. May, J.C. & McLean, J.A. Ion mobility-mass spectrometry: time-dispersive instrumentation. Anal. Chem. 87, 1422-1436 (2015).
17. Kanu, A.B., Dwivedi, P., Tam, M., Matz, L. & Hill, H.H. Jr. Ion mobility-mass spectrometry. J. Mass Spectrom. 43, 1-22 (2008).
18. Lanucara, F., Holman, S.W., Gray, C.J. & Eyers, C.E. The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. Nat. Chem. 6, 281-294 (2014).
19. Chong, W.P. et al. Metabolomics profiling of extracellular metabolites in recombinant Chinese hamster ovary fed-batch culture. Rapid Commun. Mass Spectrom. 23, 3763-3771 (2009).
20. Paglia, G. et al. Ion-mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification. Anal. Chem. 87, 1137-1144 (2015).
21. Pacini, T. et al. Multidimensional analytical approach based on UHPLC-UV-ion mobility-MS for the screening of natural pigments. Anal. Chem. 87, 2593-2599 (2015).
22. Paglia, G. et al. Ion mobility derived collision cross sections to support metabolomics applications. Anal. Chem. 86, 3985-3993 (2014).
23. Ibrahim, Y.M. et al. Development of a new ion mobility (Quadrupole) time-of-flight mass spectrometer. Int. J. Mass Spectrom. 377, 655-662 (2015).
24. Giles, K. Travelling wave ion mobility. Int. J. Ion Mobil. Spectrom. 16, 1-67 (2013).
25. Shvartsburg, A.A. & Smith, R.D. Fundamentals of traveling wave ion mobility spectrometry. Anal. Chem. 80, 9689-9699 (2008).
26. Shvartsburg, A.A. Differential Mobility Spectrometry: Nonlinear Ion Transport and Fundamentals of FAIMS (CRC Press, 2008).
27. Michelmann, K., Silveira, J.A., Ridgeway, M.E. & Park, M.A. Fundamentals of trapped ion mobility spectrometry. J. Am. Soc. Mass Spectrom. 26, 14-24 (2015).
28. Hernandez, D.R. et al. Ion dynamics in a trapped ion mobility spectrometer. Analyst 139, 1913-1921 (2014).
29. Fernandez-Lima, F., Kaplan, D.A., Suetering, J. & Park, M.A. Gas-phase separation using a trapped ion mobility spectrometer. Int. J. Ion Mobil. Spectrom. 14, 93-98 (2011).
30. Baker, P.R., Armando, A.M., Campbell, J.L., Quehenberger, O. & Dennis, E.A. Three-dimensional enhanced lipidomics analysis combining UPLC, differential ion mobility spectrometry, and mass spectrometric separation strategies. J. of Lipid Res. 55, 2432-2442 (2014).
31. Lintonen, T.P. et al. Differential mobility spectrometry-driven shotgun lipidomics. Anal. Chem. 86, 9662-9669 (2014).
32. Ruotolo, B.T., Benesch, J.L., Sandercock, A.M., Hyung, S.J. & Robinson, C.V. Ion mobility-mass spectrometry analysis of large protein complexes. Nat. Protoc. 3, 1139-1152 (2008).
33. Michaelevski, I., Kirshenbaum, N. & Sharon, M. T-wave ion mobility-mass spectrometry: basic experimental procedures for protein complex analysis. J. Vis. Exp. 41, e1985 (2010).
34. May, J.C. et al. Conformational ordering of biomolecules in the gas phase: nitrogen collision cross sections measured on a prototype high resolution drift tube ion mobility-mass spectrometer. Anal. Chem. 86, 2107-2116 (2014).
35. Paglia, G., Kliman, M., Claude, E., Geromanos, S. & Astarita, G. Applications of ion-mobility mass spectrometry for lipid analysis. Anal. Bioanal. Chem. 407, 4995-5007 (2015).
36. Paglia, G. et al. Unbiased metabolomic investigation of Alzheimer's disease brain points to dysregulation of mitochondrial aspartate metabolism. J. Proteome Res. 15, 608-618 (2016).
37. Fahy, E. et al. Update of the LIPID MAPS comprehensive classification system for lipids. J. Lipid Res. 50, S9-S14 (2009).
38. Quehenberger, O. et al. Lipidomics reveals a remarkable diversity of lipids in human plasma. J. Lipid Res. 51, 3299-3305 (2010).
39. Quehenberger, O. & Dennis, E.A. The human plasma lipidome. N. Engl. J. Med. 365, 1812-1823 (2011).
40. Wenk, M.R. The emerging field of lipidomics. Nat. Rev. Drug Discov. 4, 594-610 (2005).
41. Witting, M., Maier, T.V., Garvis, S. & Schmitt-Kopplin, P. Optimizing a ultrahigh pressure liquid chromatography-time of flight-mass spectrometry approach using a novel sub-2mum core-shell particle for in depth lipidomic profiling of Caenorhabditis elegans. J. Chromatogr. A 1359, 91-99 (2014).
42. Brown, H.A. & Murphy, R.C. Working towards an exegesis for lipids in biology. Nat. Chem. Biol. 5, 602-606 (2009).
43. Shevchenko, A. & Simons, K. Lipidomics: coming to grips with lipid diversity. Nat. Rev. Mol. Cell Biol. 11, 593-598 (2010).
44. Fenn, L.S., Kliman, M., Mahsut, A., Zhao, S.R. & McLean, J.A. Characterizing ion mobility-mass spectrometry conformation space for the analysis of complex biological samples. Anal. Bioanal. Chem. 394, 235-244 (2009).
45. Kliman, M., May, J.C. & McLean, J.A. Lipid analysis and lipidomics by structurally selective ion mobility-mass spectrometry. Biochim. Biophys. Acta 1811, 935-945 (2011).
46. Woods, A.S. et al. Lipid/peptide/nucleotide separation with MALDI-ion mobility-TOF MS. Anal. Chem. 76, 2187-2195 (2004).
47. Jackson, S.N. et al. A study of phospholipids by ion mobility TOFMS. J. Am. Soc. Mass Spectrom. 19, 1655-1662 (2008).
48. Shvartsburg, A.A., Isaac, G., Leveque, N., Smith, R.D. & Metz, T.O. Separation and classification of lipids using differential ion mobility spectrometry. J. Am. Soc. Mass Spectrom. 22, 1146-1155 (2011).
49. Leng, J. et al. Direct infusion electrospray ionization-ion mobility-mass spectrometry for comparative profiling of fatty acids based on stable isotope labeling. Anal. Chim. Acta 887, 148-154 (2015).
50. Silveira, J.A., Ridgeway, M.E. & Park, M.A. High resolution trapped ion mobility spectrometery of peptides. Anal. Chem. 86, 5624-5627 (2014).
51. Mason, E.A.M. & McDaniel, E.W. Transport Properties of Ions in Gases (Wiley, 1998).
52. Zhang, F., Guo, S., Zhang, M., Zhang, Z. & Guo, Y. Characterizing ion mobility and collision cross section of fatty acids using electrospray ion mobility mass spectrometry. J. Mass Spectrom. 50, 906-913 (2015).
53. Williams, J.P. et al. Isomer separation and gas-phase configurations of organoruthenium anticancer complexes: ion mobility mass spectrometry and modeling. J. Am. Soc. Mass Spectrom. 20, 1119-1122 (2009).
54. Bush, M.F., Campuzano, I.D. & Robinson, C.V. Ion mobility mass spectrometry of peptide ions: effects of drift gas and calibration strategies. Anal. Chem. 84, 7124-7130 (2012).
55. Campuzano, I. et al. Structural characterization of drug-like compounds by ion mobility mass spectrometry: comparison of theoretical and experimentally derived nitrogen collision cross sections. Anal. Chem. 84, 1026-1033 (2012).
56. Skraskova, K. et al. Enhanced capabilities for imaging gangliosides in murine brain with matrix-assisted laser desorption/ionization and desorption electrospray ionization mass spectrometry coupled to ion mobility separation. Methods 104, 69-78 (2016).
57. Gonzales, G.B. et al. Ultra(high)-pressure liquid chromatography-electrospray ionization-time-of-flight-ion mobility-high definition mass spectrometry for the rapid identification and structural characterization of flavonoid glycosides from cauliflower waste. J. Chromatogr. A 1323, 39-48 (2014).
58. Dear, G.J. et al. Sites of metabolic substitution: investigating metabolite structures utilising ion mobility and molecular modelling. Rapid Commun. Mass Spectrom. 24, 3157-3162 (2010).
59. Giles, K. et al. Applications of a travelling wave-based radio-frequency-only stacked ring ion guide. Rapid Commun. Mass Spectrom. 18, 2401-2414 (2004).
60. Wishart, D.S. et al. HMDB 3.0-the human metabolome database in 2013. Nucleic Acids Res. 41, D801-D807 (2013).
61. Kind, T. et al. LipidBlast in silico tandem mass spectrometry database for lipid identification. Nat. Methods 10, 755-758 (2013).
62. Smith, C.A. et al. METLIN: a metabolite mass spectral database. Ther. Drug Monit. 27, 747-751 (2005).
63. Hines, K.M., May, J.C., McLean, J.A. & Xu, L. Evaluation of collision cross section calibrants for structural analysis of lipids by traveling wave ion mobility-mass spectrometry. Anal. Chem. 88, 7329-7336 (2016).
64. Menikarachchi, L.C. et al. MolFind: a software package enabling HPLC/MS-based identification of unknown chemical structures. Anal. Chem. 84, 9388-9394 (2012).