79
46. Soga T, Ohashi Y, Ueno Y, Naraoka H, Tomita M, Nishioka T (2003) Quantitative metabolome
analysis using capillary electrophoresis mass spectrometry. J Proteome Res 2(5):488–494.
https://doi.org/10.1021/pr034020m
47. Nowak PM, Woźniakiewicz M, Gładysz M, Janus M, Kościelniak P (2017) Improving repeatability of capillary electrophoresis—a critical comparison of ten different capillary inner surfaces and three criteria of peak identification. Anal Bioanal Chem 409(18):4383–4393. https://
doi.org/10.1007/s00216-017-0382-y
48. Dwivedi P, Wu P, Klopsch SJ, Puzon GJ, Xun L, Hill HH (2008) Metabolic profiling by Ion
Mobility Mass Spectrometry (IMMS). Metabolomics 4(1):63–80. https://doi.org/10.1007/
s11306-007-0093-z
49. Miller RA, Eiceman GA, Nazarov EG, King AT (2000) Novel micromachined high-field
asymmetric waveform-ion mobility spectrometer. Sensors Actuators B Chem 67(3):300–306.
https://doi.org/10.1016/S0925-4005(00)00535-9
50. Kanu AB, Dwivedi P, Tam M, Matz L, Hill HH (2008) Ion mobility-mass spectrometry. J Mass
Spectrom 43(1):1–22. https://doi.org/10.1002/jms.1383
51. Berm EJJ, Paardekooper J, Brummel-Mulder E, Hak E, Wilffert B, Maring JG (2015) A simple
dried blood Spot method for therapeutic drug monitoring of the tricyclic antidepressants amitriptyline, nortriptyline, imipramine, clomipramine, and their active metabolites using LC-MS/
MS. Talanta 134:165–172. https://doi.org/10.1016/j.talanta.2014.10.041
52. Tautenhahn R, Bottcher C, Neumann S (2008) Highly sensitive feature detection for high
resolution LC/MS. BMC Bioinf 9. https://doi.org/10.1186/1471-2105-9-504
53. Zhang X, Quinn K, Cruickshank-Quinn C, Reisdorph R, Reisdorph N (2018) The application
of ion mobility mass spectrometry to metabolomics. Curr Opin Chem Biol:60–66. https://doi.
org/10.1016/j.cbpa.2017.11.001
54. Picache JA, Rose BS, Balinski A, Leaptrot KL, Sherrod SD, May JC, McLean JA (2019)
Collision cross section compendium to annotate and predict multi-Omic compound identities.
Chem Sci 10(4):983–993. https://doi.org/10.1039/c8sc04396e
55. Xiao JF, Zhou B, Ressom HW (2012) Metabolite identification and quantitation in LC-MS/
MS-based metabolomics. TrAC Trends Anal Chem:1–14. https://doi.org/10.1016/j.
trac.2011.08.009
56. Yost RA, Enke CG (1978) Selected ion fragmentation with a tandem quadrupole mass spectrometer. J Am Chem Soc 100(7):2274–2275. https://doi.org/10.1021/ja00475a072
57. Matraszek-Zuchowska I, Wozniak B, Posyniak A (2016) Comparison of the multiple reaction monitoring and enhanced product ion scan modes for confirmation of stilbenes in bovine
urine samples using LC–MS/MS QTRAP
® system. Chromatographia 79(15–16):1003–1012.
https://doi.org/10.1007/s10337-016-3121-1
58. Hopfgartner G, Varesio E, Tschäppät V, Grivet C, Bourgogne E, Leuthold LA (2004) Triple
quadrupole linear ion trap mass spectrometer for the analysis of small molecules and macromolecules. J Mass Spectrom 39(8):845–855. https://doi.org/10.1002/jms.659
59. Zhou J, Yin Y (2016) Strategies for large-scale targeted metabolomics quantification by liquid chromatography-mass spectrometry. Analyst 141(23):6362–6373. https://doi.org/10.1039/
c6an01753c
60. Bateman NW, Goulding SP, Shulman NJ, Gadok AK, Szumlinski KK, MacCoss MJ, Wu
CC (2014) Maximizing peptide identification events in proteomic workflows using DataDependent Acquisition (DDA). Mol Cell Proteomics 13(1):329–338. https://doi.org/10.1074/
mcp.M112.026500
61. Mullard G, Allwood JW, Weber R, Brown M, Begley P, Hollywood KA, Jones M, Unwin RD,
Bishop PN, Cooper GJS et al (2015) A new strategy for MS/MS data acquisition applying multiple data dependent experiments on orbitrap mass spectrometers in non-targeted metabolomic
applications. Metabolomics 11(5):1068–1080. https://doi.org/10.1007/s11306-014-0763-6
62. Schwudke D, Liebisch G, Herzog R, Schmitz G, Shevchenko A (2007) Shotgun lipidomics by tandem mass spectrometry under data-dependent acquisition control. Methods
Enzymol:175–191. https://doi.org/10.1016/S0076-6879(07)33010-3
4 Fundamentals of Mass Spectrometry-Based Metabolomics
46. Soga T, Ohashi Y, Ueno Y, Naraoka H, Tomita M, Nishioka T (2003) Quantitative metabolome
analysis using capillary electrophoresis mass spectrometry. J Proteome Res 2(5):488–494.
https://doi.org/10.1021/pr034020m
47. Nowak PM, Woźniakiewicz M, Gładysz M, Janus M, Kościelniak P (2017) Improving repeatability of capillary electrophoresis—a critical comparison of ten different capillary inner surfaces and three criteria of peak identification. Anal Bioanal Chem 409(18):4383–4393. https://
doi.org/10.1007/s00216-017-0382-y
48. Dwivedi P, Wu P, Klopsch SJ, Puzon GJ, Xun L, Hill HH (2008) Metabolic profiling by Ion
Mobility Mass Spectrometry (IMMS). Metabolomics 4(1):63–80. https://doi.org/10.1007/
s11306-007-0093-z
49. Miller RA, Eiceman GA, Nazarov EG, King AT (2000) Novel micromachined high-field
asymmetric waveform-ion mobility spectrometer. Sensors Actuators B Chem 67(3):300–306.
https://doi.org/10.1016/S0925-4005(00)00535-9
50. Kanu AB, Dwivedi P, Tam M, Matz L, Hill HH (2008) Ion mobility-mass spectrometry. J Mass
Spectrom 43(1):1–22. https://doi.org/10.1002/jms.1383
51. Berm EJJ, Paardekooper J, Brummel-Mulder E, Hak E, Wilffert B, Maring JG (2015) A simple
dried blood Spot method for therapeutic drug monitoring of the tricyclic antidepressants amitriptyline, nortriptyline, imipramine, clomipramine, and their active metabolites using LC-MS/
MS. Talanta 134:165–172. https://doi.org/10.1016/j.talanta.2014.10.041
52. Tautenhahn R, Bottcher C, Neumann S (2008) Highly sensitive feature detection for high
resolution LC/MS. BMC Bioinf 9. https://doi.org/10.1186/1471-2105-9-504
53. Zhang X, Quinn K, Cruickshank-Quinn C, Reisdorph R, Reisdorph N (2018) The application
of ion mobility mass spectrometry to metabolomics. Curr Opin Chem Biol:60–66. https://doi.
org/10.1016/j.cbpa.2017.11.001
54. Picache JA, Rose BS, Balinski A, Leaptrot KL, Sherrod SD, May JC, McLean JA (2019)
Collision cross section compendium to annotate and predict multi-Omic compound identities.
Chem Sci 10(4):983–993. https://doi.org/10.1039/c8sc04396e
55. Xiao JF, Zhou B, Ressom HW (2012) Metabolite identification and quantitation in LC-MS/
MS-based metabolomics. TrAC Trends Anal Chem:1–14. https://doi.org/10.1016/j.
trac.2011.08.009
56. Yost RA, Enke CG (1978) Selected ion fragmentation with a tandem quadrupole mass spectrometer. J Am Chem Soc 100(7):2274–2275. https://doi.org/10.1021/ja00475a072
57. Matraszek-Zuchowska I, Wozniak B, Posyniak A (2016) Comparison of the multiple reaction monitoring and enhanced product ion scan modes for confirmation of stilbenes in bovine
urine samples using LC–MS/MS QTRAP
® system. Chromatographia 79(15–16):1003–1012.
https://doi.org/10.1007/s10337-016-3121-1
58. Hopfgartner G, Varesio E, Tschäppät V, Grivet C, Bourgogne E, Leuthold LA (2004) Triple
quadrupole linear ion trap mass spectrometer for the analysis of small molecules and macromolecules. J Mass Spectrom 39(8):845–855. https://doi.org/10.1002/jms.659
59. Zhou J, Yin Y (2016) Strategies for large-scale targeted metabolomics quantification by liquid chromatography-mass spectrometry. Analyst 141(23):6362–6373. https://doi.org/10.1039/
c6an01753c
60. Bateman NW, Goulding SP, Shulman NJ, Gadok AK, Szumlinski KK, MacCoss MJ, Wu
CC (2014) Maximizing peptide identification events in proteomic workflows using DataDependent Acquisition (DDA). Mol Cell Proteomics 13(1):329–338. https://doi.org/10.1074/
mcp.M112.026500
61. Mullard G, Allwood JW, Weber R, Brown M, Begley P, Hollywood KA, Jones M, Unwin RD,
Bishop PN, Cooper GJS et al (2015) A new strategy for MS/MS data acquisition applying multiple data dependent experiments on orbitrap mass spectrometers in non-targeted metabolomic
applications. Metabolomics 11(5):1068–1080. https://doi.org/10.1007/s11306-014-0763-6
62. Schwudke D, Liebisch G, Herzog R, Schmitz G, Shevchenko A (2007) Shotgun lipidomics by tandem mass spectrometry under data-dependent acquisition control. Methods
Enzymol:175–191. https://doi.org/10.1016/S0076-6879(07)33010-3
4 Fundamentals of Mass Spectrometry-Based Metabolomics