Evaluation of standard and advanced preprocessing methods for the univariate analysis of blood serum 1H-NMR spectra

Analytical and Bioanalytical Chemistry

Volumn 398, Issue 4, 2010, Pages 1781-1790

  De Meyer, Tim ^a   Sinnaeve, Davy ^a   Van Gasse, Bjorn ^a   Rietzschel, Ernst R ^b   De Buyzere, Marc L ^b   Langlois, Michel R ^b,c   Bekaert, Sofie ^a   Martins, José C ^a   Van Criekinge, Wim ^a  

^a GHENT UNIVERSITY   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

^c General Hospital St Jan   (Belgium)

Author keywords

Binning; Bucketing; NMR metabolomics preprocessing; Normalization; Serum

Indexed keywords

BINNING; BUCKETING; METABOLOMICS; NORMALIZATION; SERUM;

BIOMOLECULES; BLOOD; GLUCOSE; METABOLISM; METABOLITES; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; RESONANCE; STANDARDS;

NUCLEAR MAGNETIC RESONANCE;

CREATININE; TRIACYLGLYCEROL;

ADULT; ANALYSIS OF VARIANCE; ARTICLE; CHEMISTRY; EVALUATION; FEMALE; GLUCOSE BLOOD LEVEL; HUMAN; MALE; METHODOLOGY; MIDDLE AGED; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SERUM; STANDARD;

ADULT; ANALYSIS OF VARIANCE; BLOOD GLUCOSE; CREATININE; FEMALE; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MALE; MIDDLE AGED; SERUM; TRIGLYCERIDES;

EID: 77957839768     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-010-4085-x     Document Type: Article

References (26)

1. JL Griffin 2003 Metabonomics: NMR spectroscopy and pattern recognition analysis of body fluids and tissues for characterisation of xenobiotic toxicity and disease diagnosis Curr Opin Chem Biol 7 648 654 1:CAS:528: DC%2BD3sXot12hsLg%3D 10.1016/j.cbpa.2003.08.008
2. E Holmes AW Nicholls JC Lindon SC Connor JC Connelly JN Haselden SJ Damment M Spraul P Neidig JK Nicholson 2000 Chemometric models for toxicity classification based on NMR spectra of biofluids Chem Res Toxicol 13 471 478 1:CAS:528:DC%2BD3cXivFejurY%3D 10.1021/tx990210t
3. 1H NMR spectroscopy and pattern recognition Anal Bioanal Chem 396 1451 1463 1:CAS:528:DC%2BD1MXhsFOnsbnP 10.1007/s00216-009-3338-z
4. E Holmes RL Loo J Stamler M Bictash IK Yap Q Chan T Ebbels M De Iorio IJ Brown KA Veselkov ML Daviglus H Kesteloot H Ueshima L Zhao JK Nicholson P Elliott 2008 Human metabolic phenotype diversity and its association with diet and blood pressure Nature 453 396 400 1:CAS:528:DC%2BD1cXlvV2qtLo%3D 10.1038/nature06882
5. Lindon JC, Holmes E, Nicholson JK (2005) An overview of metabonomics. In: Robertson DG, Lindon J, Nicholson JK, Holmes E (eds) Metabonomics in toxicity assessment. Taylor & Francis, Boca Raton
6. Q Zhao R Stoyanova S Du P Sajda TR Brown 2006 HiRes-a tool for comprehensive assessment and interpretation of metabolomic data Bioinformatics 22 2562 2564 1:CAS:528:DC%2BD28XhtVyns73E 10.1093/bioinformatics/btl428
7. J Xia N Psychogios N Young DS Wishart 2009 MetaboAnalyst: a web server for metabolomic data analysis and interpretation Nucleic Acids Res 37 W652 W660 1:CAS:528:DC%2BD1MXosFSkt7c%3D 10.1093/nar/gkp356
8. T Wang K Shao Q Chu Y Ren Y Mu L Qu J He C Jin B Xia 2009 Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis BMC Bioinform 10 83 10.1186/1471-2105-10-83
9. JL Izquierdo-Garcia I Rodriguez A Kyriazis P Villa P Barreiro M Desco J Ruiz-Cabello 2009 A novel R-package graphic user interface for the analysis of metabonomic profiles BMC Bioinform 10 363 10.1186/1471-2105-10-363
10. A Craig O Cloarec E Holmes JK Nicholson JC Lindon 2006 Scaling and normalization effects in NMR spectroscopic metabonomic data sets Anal Chem 78 2262 2267 1:CAS:528:DC%2BD28XhsFartL0%3D 10.1021/ac0519312
11. S Zhang C Zheng IR Lanza KS Nair D Raftery O Vitek 2009 Interdependence of signal processing and analysis of urine H-1 NMR spectra for metabolic profiling Anal Chem 81 6080 6088 1:CAS:528:DC%2BD1MXotFKnu7k%3D 10.1021/ac900424c
12. 1H NMR metabonomics Anal Chem 78 4281 4290 1:CAS:528:DC%2BD28XltVCgtro%3D 10.1021/ac051632c
13. T De Meyer D Sinnaeve B Van Gasse E Tsiporkova ER Rietzschel ML De Buyzere TC Gillebert S Bekaert JC Martins W Van Criekinge 2008 NMR-based characterization of metabolic alterations in hypertension using an adaptive, intelligent binning algorithm Anal Chem 80 3783 3790 10.1021/ac7025964
14. PE Anderson NV Reo NJ DelRaso TE Doom ML Raymer 2008 Gaussian binning: a new kernel-based method for processing NMR spectroscopic data for metabolomics Metabolomics 4 261 272 1:CAS:528:DC%2BD1cXhtVyis7bJ 10.1007/s11306-008-0117-3
15. RJO Torgrip J Lindberg M Linder B Karlberg SP Jacobsson J Kolmert I Gustafsson I Schuppe-Koistinen 2006 New modes of data partitioning based on PARS peak alignment for improved multivariate biomarker/biopattern detection in H-1-NMR spectroscopic metabolic profiling of urine Metabolomics 2 1 19 1:CAS:528:DC%2BD28XovFyiuro%3D 10.1007/s11306-005-0013-z
16. 1H NMR metabolomics data Anal Chem 78 4430 4442 1:CAS:528:DC%2BD28XksFKktbw%3D 10.1021/ac060209g
17. E Alm RJO Torgrip KM Aberg I Schuppe-Koistinen J Lindberg 2009 A solution to the 1D NMR alignment problem using an extended generalized fuzzy Hough transform and mode support Anal Bioanal Chem 395 213 223 1:CAS:528: DC%2BD1MXovFWru7k%3D 10.1007/s00216-009-2940-4
18. E Alm RJ Torgrip KM Aberg I Schuppe-Koistinen J Lindberg 2010 Time-resolved biomarker discovery in (1)H-NMR data using generalized fuzzy Hough transform alignment and parallel factor analysis Anal Bioanal Chem 10.1007/s0021600934215
19. KA Veselkov JC Lindon TM Ebbels D Crockford VV Volynkin E Holmes DB Davies JK Nicholson 2009 Recursive segment-wise peak alignment of biological (1)H NMR spectra for improved metabolic biomarker recovery Anal Chem 81 56 66 1:CAS:528:DC%2BD1cXhsVGnsLnJ 10.1021/ac8011544
20. Lindon JC, Nicholson JK, Everett JR (1999) NMR spectroscopy of biofluids. In: Webb GA (ed) Annual reports on NMR spectroscopy, vol 38. Academic, London
21. ER Rietzschel ML De Buyzere S Bekaert P Segers D De Bacquer L Cooman P Van Damme P Cassiman M Langlois P Van Oostveldt P Verdonck G De Backer TC Gillebert 2007 Rationale, design, methods and baseline characteristics of the Asklepios study Eur J Cardiovasc Prev Rehabil 14 179 191 10.1097/HJR. 0b013e328012c380
22. LH Lucas CK Larive PS Wilkinson S Huhn 2005 Progress toward automated metabolic profiling of human serum: comparison of CPMG and gradient-filtered NMR analytical methods J Pharm Biomed Anal 39 156 163 1:CAS:528: DC%2BD2MXntVGisb4%3D 10.1016/j.jpba.2004.09.060
23. 13C NMR spectroscopy of human blood plasma Anal Chem 67 793 811 1:CAS:528:DyaK2MXjsFajurs%3D 10.1021/ac00101a004
24. E Ritz 2007 Metabolic syndrome: an emerging threat to renal function Clin J Am Soc Nephrol 2 869 871 10.2215/CJN.02350607
25. LK Schnackenberg J Sun P Espandiari RD Holland J Hanig RD Beger 2007 Metabonomics evaluations of age-related changes in the urinary compositions of male Sprague Dawley rats and effects of data normalization methods on statistical and quantitative analysis BMC Bioinform 8 Suppl 7 S3 10.1186/1471-2105-8-S7-S3
26. RJO Torgrip KM Aberg E Alm I Schuppe-Koistinen J Lindberg 2008 A note on normalization of biofluid 1D H-1-NMR data Metabolomics 4 114 121 1:CAS:528:DC%2BD1cXlsFSnt7g%3D 10.1007/s11306-007-0102-2