Getting your peaks in line: A review of alignment methods for NMR spectral data

Metabolites

Volumn 3, Issue 2, 2013, Pages 259-276

  Vu, Trung Nghia ^a,b   Laukens, Kris ^a,b  

^a UNIVERSITY OF ANTWERP   (Belgium)

^b Biomedical Informatics Research Center Antwerp (Biomina)   (Belgium)

Author keywords

Alignment; NMR; Nuclear Magnetic Resonance; Peak shifts; Preprocessing

Indexed keywords

ALGORITHM; COMPUTER PROGRAM; EVALUATION; IMAGE QUALITY; METABOLOME; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PERFORMANCE; PH; PUBLISHING; REFERENCE DATABASE; REVIEW; SCORING SYSTEM; TEMPERATURE;

EID: 85016502755     PISSN: None     EISSN: 22181989     Source Type: Journal    
DOI: 10.3390/metabo3020259     Document Type: Review

References (43)

1. Beneduci, A.; Chidichimo, G.; Dardo, G.; Pontoni, G. Highly routinely reproducible alignment of 1H NMR spectral peaks of metabolites in huge sets of urines. Anal. Chim. Acta 2011, 685, 186-195.
2. Giskeødegård, G.F.; Bloemberg, T.G.; Postma, G.; Sitter, B.; Tessem, M.-B.; Gribbestad, I.S.; Bathen, T.F.; Buydens, L.M. C. Alignment of high resolution magic angle spinning magnetic resonance spectra using warping methods. Anal. Chim. Acta 2010, 683, 1-11.
3. Lindon, J.C.; Holmes, E.; Nicholson, J.K. Pattern recognition methods and applications in biomedical magnetic resonance. Prog. Nucl. Mag. Res. Sp. 2001, 39, 1-40.
4. Davis, R.A.; Charlton, A.J.; Godward, J.; Jones, S.A.; Harrison, M.; Wilson, J.C. Adaptive binning: An improved binning method for metabolomics data using the undecimated wavelet transform. Chemometr. Intell. Lab. Syst. 2007, 85, 144-154.
5. De Meyer, T.; Sinnaeve, D.; Van Gasse, B.; Tsiporkova, E.; Rietzschel, E.R.; De Buyzere, M.L.; Gillebert, T.C.; Bekaert, S.; Martins, J.C.; Van Criekinge, W. NMR-based characterization of metabolic alterations in hypertension using an adaptive, intelligent binning algorithm. Anal. Chem. 2008, 80, 3783-3790.
6. Anderson, P.E.; Reo, N.V.; DelRaso, N.J.; Doom, T.E.; Raymer, M.L. Gaussian binning: A new kernel-based method for processing NMR spectroscopic data for metabolomics. Metabolomics 2008, 4, 261-272.
7. Sousa, S.A.A.; Magalhães, A.; Ferreira, M.M.C. Optimized bucketing for NMR spectra: Three case studies. Chemometr. Intell. Lab. Syst. 2013, 122, 93-102.
8. Vu, T.N.; Valkenborg, D.; Smets, K.; Verwaest, K.A.; Dommisse, R.; Lemière, F.; Verschoren, A.; Goethals, B.; Laukens, K. An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics 2011, 12, 405.
9. Larsen, F.H.; Van den Berg, F.; Engelsen, S.B. An exploratory chemometric study of 1H NMR spectra of table wines. J. Chemometr. 2006, 20, 198-208.
10. Savorani, F.; Tomasi, G.; Engelsen, S.B. icoshift: A versatile tool for the rapid alignment of 1D NMR spectra. J. Magn. Reson. 2010, 202, 190-202.
11. Vogels, J.T.W.E.; Tas, A.C.; Venekamp, J.; Van der Greef, J. Partial linear fit: A new NMR spectroscopy preprocessing tool for pattern recognition applications. J. Chemometr. 1996, 10, 425-438.
12. Nielsen, N.P.V.; Carstensen, J.M.; Smedsgaard, J. Aligning of single and multiple wavelength chromatographic profiles for chemometric data analysis using correlation optimised warping. J. Chromatogr. A 1998, 805, 17-35.
13. Forshed, J.; Schuppe-Koistinen, I.; Jacobsson, S.P. Peak alignment of NMR signals by means of a genetic algorithm. Analytica. Chimica. Acta 2003, 487, 189-199.
14. Torgrip, R.J.O.; Åberg, M.; Karlberg, B.; Jacobsson, S.P. Peak alignment using reduced set mapping. J. Chemometr. 2003, 17, 573-582.
15. Tomasi, G.; Van den Berg, F.; Andersson, C. Correlation optimized warping and dynamic time warping as preprocessing methods for chromatographic data. J. Chemometr. 2004, 18, 231-241.
16. Lee, G.C.; Woodruff, D.L. Beam search for peak alignment of NMR signals. Analytica. Chimica. Acta 2004, 513, 413-416.
17. Stoyanova, R.; Nicholls, A.W.; Nicholson, J.K.; Lindon, J.C.; Brown, T.R. Automatic alignment of individual peaks in large high-resolution spectral data sets. J. Magn. Reson. 2004, 170, 329-335.
18. Eilers, P.H.C. Parametric Time Warping. Anal. Chem. 2004, 76, 404-411.
19. Wong, J.W.H.; Durante, C.; Cartwright, H.M. Application of fast Fourier transform cross-correlation for the alignment of large chromatographic and spectral datasets. Anal. Chem. 2005, 77, 5655-5661.
20. Wong, J.W.H.; Cagney, G.; Cartwright, H.M. SpecAlign-processing and alignment of mass spectra datasets. Bioinformatics 2005, 21, 2088-2090.
21. Wu, W.; Daszykowski, M.; Walczak, B.; Sweatman, B.C.; Connor, S.C.; Haselden, J.N.; Crowther, D.J.; Gill, R.W.; Lutz, M.W. Peak alignment of urine NMR spectra using fuzzy warping. J. Chem. Inf. Model. 2006, 46, 863-875.
22. Csenki, L.; Alm, E.; Torgrip, R.J.O.; Aberg, K.M.; Nord, L.I.; Schuppe-Koistinen, I.; Lindberg, J. Proof of principle of a generalized fuzzy Hough transform approach to peak alignment of one-dimensional 1H NMR data. Anal. Bioanal. Chem. 2007, 389, 875-885.
23. Veselkov, K.A.; Lindon, J.C.; Ebbels, T.M. D.; Crockford, D.; Volynkin, V.V.; Holmes, E.; Davies, D.B.; Nicholson, J.K. Recursive segment-wise peak alignment of biological 1H NMR spectra for improved metabolic biomarker recovery. Anal. Chem. 2009, 81, 56-66.
24. Staab, J.M.; O'Connell, T.M.; Gomez, S.M. Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS). BMC Bioinformatics 2010, 11, 123.
25. Kim, S.B.; Wang, Z.; Hiremath, B. A Bayesian approach for the alignment of high-resolution NMR spectra. Ann. Oper. Res. 2010, 174, 19-32.
26. Wang, T.; Shao, K.; Chu, Q.; Ren, Y.; Mu, Y.; Qu, L.; He, J.; Jin, C.; Xia, B. Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis. BMC Bioinformatics 2009, 10, 83.
27. Yang, C.; He, Z.; Yu, W. Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis. BMC Bioinformatics 2009, 10, 4.
28. Skov, T.; Van den Berg, F.; Tomasi, G.; Bro, R. Automated alignment of chromatographic data. J. Chemometr. 2006, 20, 484-497.
29. MacKinnon, N.; Ge, W.; Khan, A.P.; Somashekar, B.S.; Tripathi, P.; Siddiqui, J.; Wei, J.T.; Chinnaiyan, A.M.; Rajendiran, T.M.; Ramamoorthy, A. Variable reference alignment: An improved peak alignment protocol for NMR spectral data with large intersample variation. Anal. Chem. 2012, 84, 5372-5379.
30. Alm, E.; Torgrip, R.J.O.; Aberg, K.M.; Schuppe-Koistinen, I.; Lindberg, J. A solution to the 1D NMR alignment problem using an extended generalized fuzzy Hough transform and mode support. Anal. Bioanal. Chem. 2009, 395, 213-223.
31. Clifford, D.; Stone, G.; Montoliu, I.; Rezzi, S.; Martin, F.P.; Guy, P.; Bruce, S.; Kochhar, S. Alignment using variable penalty dynamic time warping. Anal. Chem. 2009, 81, 1000-1007.
32. Burges, C.J.C. A Tutorial on Support Vector Machines for Pattern Recognition. Data Min. Knowl. Discov. 1998, 2, 121-167.
33. Vapnik, V.N. The nature of statistical learning theory; Springer-Verlag New York, Inc.: New York, NY, USA, 1995.
34. Breiman, L. Random Forests. Mach. Learn. 2001, 45, 5-32.
35. Barker, M.; Rayens, W. Partial least squares for discrimination. J. Chemometr. 2003, 17, 166-173.
36. Smolinska, A.; Blanchet, L.; Buydens, L.M. C.; Wijmenga, S.S. NMR and pattern recognition methods in metabolomics: from data acquisition to biomarker discovery: a review. Anal. Chim. Acta 2012, 750, 82-97.
37. Cloarec, O.; Dumas, M.E.; Trygg, J.; Craig, A.; Barton, R.H.; Lindon, J.C.; Nicholson, J.K.; Holmes, E. Evaluation of the orthogonal projection on latent structure model limitations caused by chemical shift variability and improved visualization of biomarker changes in 1H NMR spectroscopic metabonomic studies. Anal. Chem. 2005, 77, 517-526.
38. Forshed, J.; Torgrip, R.J.O.; Åberg, K.M.; Karlberg, B.; Lindberg, J.; Jacobsson, S.P. A comparison of methods for alignment of NMR peaks in the context of cluster analysis. J Pharmaceut. Biomed. Anal. 2005, 38, 824-832.
39. Cloarec, O.; Dumas, M.E.; Craig, A.; Barton, R.H.; Trygg, J.; Hudson, J.; Blancher, C.; Gauguier, D.; Lindon, J.C.; Holmes, E.; et al. Statistical Total Correlation Spectroscopy: An exploratory approach for latent biomarker identification from metabolic 1H NMR data sets. Anal. Chem. 2005, 77, 1282-1289.
40. Holmes, E.; Cloarec, O.; Nicholson, J.K. Probing Latent Biomarker Signatures and in Vivo Pathway Activity in Experimental Disease States via Statistical Total Correlation Spectroscopy (STOCSY) of Biofluids: Application to HgCl2 toxicity. J. Proteome Res. 2006, 5, 1313-1320.
41. Torgrip, R.J.O.; Alm, E.; Åberg, K.M. Warping and alignment technologies for inter-sample feature correspondence in 1D H-NMR, chromatography-, and capillary electrophoresis-mass spectrometry data. Bioanal. Rev. 2010, 1, 105-116.
42. Zheng, M.; Lu, P.; Liu, Y.; Pease, J.; Usuka, J.; Liao, G.; Peltz, G. 2D NMR metabonomic analysis: a novel method for automated peak alignment. Bioinformatics 2007, 23, 2926-2933.
43. Robinette, S.L.; Ajredini, R.; Rasheed, H.; Zeinomar, A.; Schroeder, F.C.; Dossey, A.T.; Edison, A.S. Hierarchical alignment and full resolution pattern recognition of 2D NMR Spectra: application to nematode chemical ecology. Anal. Chem. 2011, 83, 1649-1657.