Global metabolic profiling procedures for urine using UPLC-MS.
The production of 'global' metabolite profiles involves measuring low molecular-weight metabolites (<1 kDa) in complex biofluids/tissues to study perturbations in response to physiological challenges, toxic insults or disease processes. Information-rich analytical platforms, such as mass spectrometry (MS), are needed. Here we describe the application of ultra-performance liquid chromatography-MS (UPLC-MS) to urinary metabolite profiling, including sample preparation, stability/storage and the selection of chromatographic conditions that balance metabolome coverage, chromatographic resolution and throughput. We discuss quality control and metabolite identification, as well as provide details of multivariate data analysis approaches for analyzing such MS data. Using this protocol, the analysis of a sample set in 96-well plate format, would take ca. 30 h, including 1 h for system setup, 1-2 h for sample preparation, 24 h for UPLC-MS analysis and 1-2 h for initial data processing. The use of UPLC-MS for metabolic profiling in this way is not faster than the conventional HPLC-based methods but, because of improved chromatographic performance, provides superior metabolome coverage.
Want
Elizabeth J
EJ
Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK. e.want@imperial.ac.uk
Wilson
Ian D
ID
Gika
Helen
H
Theodoridis
Georgios
G
Plumb
Robert S
RS
Shockcor
John
J
Holmes
Elaine
E
Nicholson
Jeremy K
JK
D015415:Biomarkers / Q000652:urine; D002853:Chromatography, Liquid / Q000379:methods*; D006801:Humans; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D015394:Molecular Structure; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D014556:Urine / Q000737:chemistry*
D015415:Biomarkers
Anal Chem. 2006 Feb 1;78(3):779-87
16448051
Rapid Commun Mass Spectrom. 2006;20(13):1989-94
16755610
J Chromatogr Sci. 2008 Mar;46(3):209-14
18334086
Anal Chem. 2006 Jul 1;78(13):4334-41
16808440
J Chromatogr B Biomed Sci Appl. 2000 Oct 1;748(1):281-93
11092605
Drugs R D. 2008;9(5):307-22
18721000
Anal Chem. 2008 Jan 15;80(2):421-9
18085752
Anal Chem. 2007 Dec 1;79(23):8911-8
17973349
J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jun 15;789(2):283-301
12742120
J Mass Spectrom. 2008 Feb;43(2):251-61
17968853
Anal Chem. 2006 Feb 1;78(3):743-52
16448047
Anal Chem. 2008 Nov 1;80(21):8045-54
18834150
Analyst. 2005 Jun;130(6):844-9
15912231
Nature. 2008 May 15;453(7193):396-400
18425110
Anal Chem. 1996 Dec 15;68(24):4431-5
8972626
Anal Chem. 2006 Oct 15;78(20):7278-83
17037933
Nat Rev Drug Discov. 2002 Feb;1(2):153-61
12120097
Nature. 2008 Oct 23;455(7216):1054-6
18948945
J Chromatogr A. 2008 May 2;1189(1-2):314-22
18096175
Anal Chem. 1998 Mar 1;70(5):882-9
9511465
Mass Spectrom Rev. 2008 Nov-Dec;27(6):661-99
18683895
Ther Drug Monit. 2005 Dec;27(6):747-51
16404815
Anal Chem. 2006 Jan 15;78(2):363-71
16408915
Anal Chem. 2009 Feb 15;81(4):1357-64
19170513
Toxicol Pathol. 2008 Jan;36(1):140-7
18337232
J Sep Sci. 2008 May;31(9):1598-608
18461568
Expert Rev Mol Diagn. 2008 Sep;8(5):617-33
18785810
Methods Mol Biol. 2007;406:409-36
18287705
J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Aug 15;871(2):299-305
18579458
J Proteome Res. 2005 Mar-Apr;4(2):591-8
15822939
BMC Bioinformatics. 2009 Jul 21;10:227
19622150
Analyst. 2006 Oct;131(10):1075-8
17003852
Chem Res Toxicol. 2008 Jan;21(1):9-27
18171018
Anal Chem. 2003 Mar 15;75(6):1536-41
12659219
Nat Protoc. 2007;2(11):2692-703
18007604
J Chromatogr B Biomed Sci Appl. 2000 Oct 1;748(1):269-79
11092604
J Exp Bot. 2005 Jan;56(410):219-43
15618298
Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6
17202168
Anal Chem. 2007 Feb 1;79(3):1181-6
17263352
J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Dec 15;828(1-2):9-13
16181815
Nucleic Acids Res. 2009 Jan;37(Database issue):D603-10
18953024
Plant Biotechnol J. 2006 Jul;4(4):381-92
17177804
BMC Bioinformatics. 2006 Dec 13;7:530
17166258
Curr Neurovasc Res. 2007 Nov;4(4):280-8
18045154
Rapid Commun Mass Spectrom. 2009 Apr;23(7):1085-94
19263405
J Chromatogr A. 2006 Jul 7;1120(1-2):13-20
16580006
Analyst. 2004 Jun;129(6):535-41
15152332
Anal Biochem. 2001 Apr 15;291(2):245-52
11401298
Pharm Res. 2007 Oct;24(10):1962-73
17458684
PLoS Genet. 2008 Nov;4(11):e1000282
19043545
J Proteome Res. 2007 Aug;6(8):3291-303
17625818
Anal Chem. 1993 Feb 15;65(4):327-30
8382454
Toxicol Appl Pharmacol. 2005 Apr 15;204(2):135-51
15808519
Xenobiotica. 1999 Nov;29(11):1181-9
10598751
J Chromatogr A. 2007 Jul 27;1158(1-2):318-28
17466315
Plant Mol Biol. 2002 Jan;48(1-2):155-71
11860207
Rapid Commun Mass Spectrom. 2007;21(9):1485-96
17394128
Anal Chem. 1987 Dec 1;59(23):2830-2
3434810
Bioinformatics. 2003 Nov 22;19(17):2283-93
14630657
J Chromatogr A. 2007 Mar 16;1144(2):161-9
17303144
J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Aug 15;871(2):253-60
18490203
Xenobiotica. 2006 Jul;36(7):615-29
16864507
J Proteome Res. 2007 Feb;6(2):459-68
17269703
Methods Mol Biol. 2006;324:159-75
16761377
J Pharm Biomed Anal. 2004 Nov 19;36(4):841-9
15533678
J Chromatogr A. 2001 Dec 7;937(1-2):41-7
11765083
J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Aug 15;871(2):279-87
18485837
FEBS J. 2007 Mar;274(5):1140-51
17298438
Int J Epidemiol. 2008 Apr;37 Suppl 1:i31-40
18381391
J Chromatogr. 1977 Sep 1;143(5):427-62
330556
Anal Chem. 2001 Dec 1;73(23):5635-44
11774901
Bioinformatics. 2006 Mar 1;22(5):634-6
16403790
J Proteome Res. 2009 Apr;8(4):2114-21
19714883
Anal Chem. 2008 Sep 15;80(18):6835-44
18700783
Anal Bioanal Chem. 2007 Nov;389(5):1469-75
17922113
Anal Biochem. 2002 Feb 15;301(2):298-307
11814300
J Proteome Res. 2009 Jan;8(1):170-7
19072164
Anal Biochem. 2007 Apr 15;363(2):185-95
17316536