Retention time alignment algorithms for LC/MS data must consider non-linear shifts

Bioinformatics

Volumn 25, Issue 6, 2009, Pages 758-764

  Podwojski, Katharina ^a,b   Fritsch, Arno ^a   Chamrad, Daniel C ^c   Paul, Wolfgang ^a,b   Sitek, Barbara ^b,d   Stühler, Kai ^b,d   Mutzel, Petra ^a   Stephan, Christian ^d   Meyer, Helmut E ^d   Urfer, Wolfgang ^a   Ickstadt, Katja ^a   Rahnenföhrer, Jörg ^a  

^a TU DORTMUND UNIVERSITY   (Germany)

^b Zentrum für Angewandte Proteomik   (Germany)

^c PROTAGEN AG   (Germany)

^d RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ALIGNMENT ALGORITHM; ARTICLE; COMPUTER SIMULATION; CONTROLLED STUDY; INFORMATION PROCESSING; LINEAR REGRESSION ANALYSIS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONLINEAR SYSTEM; PRIORITY JOURNAL; PROTEOMICS;

ALGORITHMS; CHROMATOGRAPHY, LIQUID; COMPUTER SIMULATION; MASS SPECTROMETRY; PROTEINS; PROTEOME; PROTEOMICS;

EID: 62549154087     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp052     Document Type: Article

References (20)

1. Christin,C. et al. (2008) Optimized time alignment algorithm for LC-MS data: Correlation optimized warping using component detection algorithm-selected mass chromatograms. Anal. Chem., 80, 7012-7021.
2. Cleveland,W. et al. (1992) Chapter 8: Local regression models. In Statistical Models in S. Chambers,J. and Hastie,T. eds, Pacific Grove, California. Wadsworth and Brooks/Cole Advanced Books and Software.
3. Everitt,B. (1986) Cluster Analysis. Gower, Aldershot, England.
4. Hastie,T. et al. (2001) The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Springer-Verlag, New York.
5. Hurvich,C. et al. (1998) Smoothing parameter selection in nonparametric regression using an improved Akaike Information Criterion. J. R. Stat. Soc. Series B, 60, 271-293.
6. Lange,E. et al. (2007) A geometric approach for the alignment of liquid chromatography-mass spectrometry data. Bioinformatics, 23, i273-i281.
7. Lange,E. et al. (2008) Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements. BMC Bioinformatics, 9, 375.
8. Listgarten,J. and Emili,A. (2005) Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteom., 4, 419-434.
9. Listgarten,J. et al. (2006) Difference detection in LC-MS data for protein biomarker discovery. Bioinformatics, 23, e198-e204.
10. Meyer,H. and Stühler,K. (2007) High-performance proteomics as a tool in biomarker discovery. Proteomics, 7 (Suppl. 1), 18-26.
11. Podwojski,K. et al. (2008) A retention-time alignment algorithm for LC/MS data. In Proceedings of the Fifth International Workshop on Computational Systems Biology. Ahdesmäki,M. et al. eds, TICSP series # 41. Tampere, Finland, pp. 129-132.
12. R Development Core Team (2008) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
13. Radulovic,D. et al. (2004) Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteom., 3 984-997.
14. Schwarz,G. (1978) Estimating the dimension of a model. Ann. Stat., 6, 461-464.
15. Smith,C. et al. (2006) XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem., 78, 779-787.
16. Suits,F. et al. (2008) Two-dimensional method for time aligning liquid chromatographymass spectrometry data. Anal. Chem., 80 3095-3104.
17. Tomasi,G. et al. (2004) Correlation optimized warping and dynamic time warping as pre-processing methods for chromatographic data. J. Chemometr., 18, 231-241.
18. Vandenbogaert,M. et al. (2008) Alignment of LC-MS images, with applications to biomarker discovery and protein identification. Proteomics, 8, 650-672.
19. van Nederkassel,A. et al. (2006) A comparison of three algorithms for chromatographic alignment. J. Chromatogr. A, 1118, 199-210.
20. Wang,P. et al. (2007) A statistical method for chromatographic alignment of LC-MS data. Biostatistics, 8, 357-367.