Magnus Åberg
Title: Alignment and Warping - Solving the correspondence problem for metabonomics data sets
Recommended Reading
• Synchronization of batch trajectories using dynamic time warping, Athanassios Kassidas, John F. MacGregor, Paul A. Taylor, AIChE Journal 44(4), 864-875, 1998. (doi: 10.1002/aic.690440412)
• Aligning of single and multiple wavelength chromatographic profiles for chemometric data analysis using correlation optimised warping, Niels-Peter Vest Nielsen, Jens Michael Carstensen and Jørn Smedsgaard, J. Chrom. A 805(1-2), 17-35, 1998. (doi:10.1016/S0021-9673(98)00021-1)
• Correlation optimized warping and dynamic time warping as preprocessing methods for chromatographic data, Giorgio Tomasi, Frans van den Berg and Claus Andersson, J. of Chemom. 18(5), 231-241, 2004. (doi: 10.1002/cem.859)
• Partial linear fit: A new NMR spectroscopy preprocessing tool for pattern recognition applications, J. T. W. E. Vogels, A. C. Tas, J. Venekamp, J. van der Greef, J. Chemom. 10(5-6), 425-438, 1996.
(doi: 10.1002/(SICI)1099-128X(199609)10:5/6<425::AID-CEM442>3.0.CO;2-S)
• Peak alignment using reduced set mapping, Ralf J. O. Torgrip, Magnus Åberg, Bo Karlberg, Sven P. Jacobsson, J. Chemom. 17(11), 573-582, 2003. (doi: 10.1002/cem.824)
• Extensions to peak alignment using reduced set mapping: classification of LC/UV data from peptide mapping, K. Magnus Åberg, Ralf J. O. Torgrip, Sven P. Jacobsson, J. of Chemom. 18(10), 465-473, 2004. (doi: 10.1002/cem.892)
• Peak alignment of NMR signals by means of a genetic algorithm, Jenny Forshed, Ina Schuppe-Koistinen and Sven P. Jacobsson, Anal. Chim. Acta 487(2), 189-199, 2003. (doi:10.1016/S0003-2670(03)00570-1)
• Parametric Time Warping, Paul H. C. Eilers, Anal. Chem. 76 (2), 404 -411, 2004. (doi: 10.1021/ac034800e S0003-2700(03)04800-5)
• Fuzzy warping of chromatograms, Beata Walczaka and Wen Wu, Chemom. and Intell. Lab. Syst. 77(1-2), 173-180, 2005. (doi:10.1016/j.chemolab.2004.07.012)

Marc-Emmanuel Dumas
Title: Practical aspects of NMR data processing - Metabonomics as a driving force to improve post-genomic data integration: examples from insulin resistance research
Recommended Reading
• Nicholson JK, Lindon JC, Holmes E. 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data.
Xenobiotica. 1999 Nov;29(11):1181-9. Review.
• Nicholson JK, Lindon JC, Holmes E. Metabonomics: a platform for studying drug toxicity and gene function.
Nat Rev Drug Discov. 2002 Feb;1(2):153-61. Review.
• Cloarec O, Dumas ME, Trygg J, Craig A, Barton RH, Lindon JC, Nicholson JK, 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 Jan 15;77(2):517-26.
• Cloarec O, Dumas ME, Craig A, Barton RH, Trygg J, Hudson J, Blancher C, Gauguier D, Lindon JC, Holmes E, Nicholson J. Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets.
Anal Chem. 2005 Mar 1;77(5):1282-9.
• Dumas ME, Maibaum EC, Teague C, Ueshima H, Zhou B, Lindon JC, Nicholson JK, Stamler J, Elliott P, Chan Q, Holmes E. Assessment of analytical reproducibility of 1H NMR spectroscopy based metabonomics for large-scale epidemiological research: the INTERMAP Study.
Anal Chem. 2006 Apr 1;78(7):2199-208.
• Dumas ME, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside J, Tatoud R, Blanc V, Lindon JC, Mitchell SC, Holmes E, McCarthy MI, Scott J, Gauguier D, Nicholson JK. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice.
Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12511-6. Epub 2006 Aug 8.

Mattias Rantalainen
Title: Multivariate approaches to integration of Metabonomic and Proteomic data
Recommended Reading
• Trygg, J. & Wold, S. Orthogonal projections to latent structures (O-PLS). Journal of Chemometrics 16, 119-128 (2002).
• Trygg, J. & Wold, S. O2-PLS, a two-block (X-Y) latent variable regression (LVR) method with an integral OSC filter. Journal of Chemometrics 17, 53-64 (2003).
• Rantalainen, M. et al. Statistically integrated metabonomic-proteomic studies on a human prostate cancer xenograft model in mice. J Proteome Res 5, 2642-55 (2006).

Jens Lamerz
Title: Quantitative Approaches in Proteomics
Recommended Reading
• Domon B, Aebersold R. Related Articles, Mass spectrometry and protein analysis. Science. 2006 Apr 14;312(5771):212-7. Review.
• Ong SE, Foster LJ, Mann M. Related Articles, Mass spectrometric-based approaches in quantitative proteomics. Methods. 2003 Feb;29(2):124-30. Review.
• Aebersold R, Mann M. Related Articles, Mass spectrometry-based proteomics. Nature. 2003 Mar 13;422(6928):198-207. Review.
• Findlay JW, Smith WC, Lee JW, Nordblom GD, Das I, DeSilva BS, Khan MN, Bowsher RR. Validation of immunoassays for bioanalysis: a pharmaceutical industry perspective.J Pharm Biomed Anal. 2000 Jan;21(6):1249-73.

Philip Brown
Title: Bayesian Modelling and Feature Selection of Proteomic Functional Data
Recommended Reading
• Tibshirani, R. (1996): ``Regression shrinkage and selection via the lasso,''
Journal of the Royal Statistical Society B, 58, 267-288.
• Brown, P. J., Fearn, T. and Vannucci, M. (2001): ``Bayesian wavelet
regression on curves with application to a spectroscopic calibration
problem,'' Journal of the American Statistical Association,
96, 398-408.
• Morris, J. S., Vannucci, M., Brown, P. J.
and Carroll, R. J. (2003). Wavelet-based nonparametric modelling
of hierarchical functions in colon carcinogenesis. Special Chosen
Applications of Case Studies Read Paper with Discussion
Joint Statistical Meetings, San Francisco,
J Amer. Statist. Ass., 98, 573-597.
• Morris, J. S. and Carroll, R. J. (2006) Wavelet based functional mixed models.
J Roy Statist Soc B, 68(2), 179-199.

Richard H. Barton
Title: Introduction to metabonomics: principles and historical perspectives - Overview - Basic Pattern Recognition
Recommended Reading
• Nicholson JK, Lindon JC, Holmes E. 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data.
Xenobiotica. 1999 Nov;29(11):1181-9. Review.
• Nicholson JK, Lindon JC, Holmes E. Metabonomics: a platform for studying drug toxicity and gene function.
Nat Rev Drug Discov. 2002 Feb;1(2):153-61. Review.
• Cloarec O, Dumas ME, Trygg J, Craig A, Barton RH, Lindon JC, Nicholson JK, 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 Jan 15;77(2):517-26.
• Cloarec O, Dumas ME, Craig A, Barton RH, Trygg J, Hudson J, Blancher C, Gauguier D, Lindon JC, Holmes E, Nicholson J.
• Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets.
Anal Chem. 2005 Mar 1;77(5):1282-9.
• Dumas ME, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside J, Tatoud R, Blanc V, Lindon JC, Mitchell SC, Holmes E, McCarthy MI, Scott J, Gauguier D, Nicholson JK.
• Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice.
Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12511-6. Epub 2006 Aug 8.
• Martens, Harald / Næs, Tormod
Multivariate Calibration
1. Edition - April 1991
225.- Euro / 356.- SFR
1991. XVIII, 420 Pages, Softcover
ISBN-10: 0-471-93047-4
ISBN-13: 978-0-471-93047-1 - John Wiley & Sons

To Marc's set of references, I would add the weblink for the Chemometrics Homepage, run by leading Swedish Chemometrician Johan Trygg. If you want to explore the boundaries, or look for methods relevant to your special application, this site is a well-worthwhile source of information: Johan has continued and refined new methodologies in Orthogonal filtration methodology, for which I also include some historical references:
• Beckwith-Hall, B. M., Brindle. J. T., Barton, R. H., Coen, M., Holmes, E. C., Nicholson, J. K,, and Antti, H.,
• Application of Orthogonal Signals Correction to Minimise the Effects of Physical and Biological Variation in High resolution 1H NMR spectra of Biofluids.Analyst 2002, 127,1283-1288.
• Trygg, J. O2-PLS for Qualitative and Quantitative Analysis in Multivariate Calibration J. Chemom. 2002, 16, 283-293.

The website is most recently migrated to: http://www.chemometrics.se/

Bart Mertens
Title: Case-control study design and validation-based modelling for pattern classification in proteomics mass spectral data.
Logistic modelling for case-control analysis of proteomics mass
spectra classification.
Recommended Reading
• Mass Spectrometry Proteomic Diagnosis: Enacting the Double
Cross-Validatory Paradigm
Bart J.A. Mertens, M.E. De Noo, R.A.E.M. Tollenaar, A.M. Deelder
Journal of Computational Biology. Nov 2006, Vol. 13, No. 9: 1591-1605
• de Noo, M.E., Mertens, B.J. , Ozalp, A., Bladergroen, M.R.,
van der Werff, M.P.J., van de Velde, C. J., Deelder,A.M., Tollenaar,
R.A.E.M. (2006) Detection of colorectal cancer using
MALDI-TOF serum protein profiling. Eur. J. Cancer} 42, 1068-1076.
• Hand, D. J. (1997) Construction and Assessment of Classication Rules.
Chichester: Wiley. (Chapter 2)

Cinzia Stella
Title: Specificity of MS-based metabonomic data
Recommended Reading
• Wilson, I.D., Plumb, R., Granger, J., Major, H., Williams, R.,
Lenz, E.M., *HPLC-MS based methods for the study of metabonomics*
- Review, Journal of Chromatography B, 817 (2005), 67-76 (and references therein)
• Villas-Boas, S.G., Mas, S., Akesson, M., Smedsgaard, J., Nielsen,
J., *Mass spectrometry in metabolome analysis-Review,* Mass
Spectrometry Reviews, 24 (2005), 613-646 (and references therein)

Anthony Maher
Title: NMR-based metabonomic data
Recommended Reading
• Lindon JC, Holmes E, Bollard ME, Stanley EG, Nicholson JK.
Metabonomics technologies and their applications in physiological monitoring, drug safety assessment and disease diagnosis.
Biomarkers. 2004 Jan-Feb;9(1):1-31
PMID: 15204308

Mark Earll
Title: Validation of Multivariate Methods and Robustness
Recommended Reading
• Multivariate and Megavariate Data Analysis Advanced Applications and Method Extensions (Part II) (Paperback)
by L. Eriksson, E. Johansson, N. Kettaneh-Wold., J. Trygg, C. Wikstrom, S. Wold
• Analysis of gene expression datasets using partial least squares discriminant analysis and principal component analysis. U.Atif, M.Earll, L.Eriksson, E.Johansson, P.Lord and S.Margrett pp369-373 In Euro QSAR 2002 Designing Drugs and Crop Protectants: processes, problems and solutions. Editors Martyn Ford, David Livingstone, John Dearden and Han Van de Waterbeemd. Blackwell Publishing ISBN 1-4051-2561-0
• Detection of ovarian cancer using chemometric analysis of proteomic profiles Oliver P. Whelehan, Mark E. Earll, Erik Johansson, Marianne Toft, Lennart Eriksson Chemometrics and Intelligent Laboratory Systems 84 (2006) 82–87
• Chemometric contributions to the evolution of metabonomics: mathematical solutions to characterising and interpreting complex biological spectra E.Holmes and H. Antti Analyst, 2002,127,1549-1557
• O2-PLS for qualitative and quantitative analysis in multivariate calibration. Johan Trygg Journal of Chemometrics 200;16:283-293
• Summary recommendations for standardization and reporting of metabolic analyses Nature Biotechnology 23, 833 - 838 (2005) doi:10.1038/nbt0705-833
The Standard Metabolic Reporting Structures working group

Bernard Silverman
Title: Empirical Bayes thresholding:adapting to sparsity when it is advantageous to do so
Recommended Reading
• I. M. Johnstone & B. W. Silverman,
EbayesThresh: R programs for Empirical Bayes thresholding. Journal of
Statistical Software, 12.8, 1–38. (2005). (
http://www.jstatsoft.org/index.php?vol=12 )
and other papers referred to there.

Chris Holmes
Title: Bayesian methods for detecting genetical biomarkers in NMR and Mass Spectrometry data
Recommended Reading
• Bayesian Data Analysis, Gelman, A. et al (2004), Chapman & Hall

Paul Eilers
Title: Data collection and analysis for high-throughput quantitative proteomics: current status and challenges
Experimental design, measurement errors and data transformation for Proteomics and Metabonomics data
Statistical Modelling of mass spectrometry proteomic data
Multiple comparison issues and False Discovery Rate
Recommended Reading
• Coombes KR, Tsavachidis S, Morris JS, et al.
Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform
PROTEOMICS 5 (16): 4107-4117 NOV 2005
• Morris JS, Coombes KR, Koomen J, et al.
Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum
BIOINFORMATICS 21 (9): 1764-1775 MAY 1 2005
• Baggerly KA, Morris JS, Coombes KR
Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments
BIOINFORMATICS 20 (5): 777-U710 MAR 22 2004
• Coombes KR, Fritsche HA, Clarke C, et al.
Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization
CLINICAL CHEMISTRY 49 (10): 1615-1623 OCT 2003
• Baggerly KA, Morris JS, Wang J, et al.
A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples
PROTEOMICS 3 (9): 1667-1672 SEP 2003
• Jeffries N
Algorithms for alignment of mass spectrometry proteomic data
BIOINFORMATICS 21 (14): 3066-3073 JUL 15 2005
• Tan CS, Ploner A, Quandt A, et al.
Finding regions of significance in SELDI measurements for identifying protein biomarkers
BIOINFORMATICS 22 (12): 1515-1523 JUN 15 2006
• Tan CS, Ploner A, Quandt A, et al.
Annotated regions of significance of SELDI-TOF-MS spectra for detecting protein biornarkers
PROTEOMICS 6 (23): 6124-6133 DEC 2006
• de Noo ME, Tollenaar RAEM, Ozalp A, et al.
Reliability of human serum protein profiles generated with C8 magnetic beads assisted MALDI-TOF mass spectrometry
ANALYTICAL CHEMISTRY 77 (22): 7232-7241 NOV 15 2005
• Eilers PHC
Parametric time warping
ANALYTICAL CHEMISTRY 76 (2): 404-411 JAN 15 2004
• Eilers PHC
A perfect smoother
ANALYTICAL CHEMISTRY 75 (14): 3631-3636 JUL 15 2003

Nathan Edwards
Title: Statistical significance for peptide identification by tandem mass spectrometry
Recommended Reading
•

George Nicholson
Title: Lessons from MolPAGE on analysis of proteomics and metabonomics data on the same samples
Recommended Reading
• Coombes, K. R. et al., (2005), Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform,Proteomics 5,4107-4117.
• Morris, J. S. et al., (2005), Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum, Bioinformatics, 21 (9) 1764-1775
• Listgarten, J. and Emili., A. (2005) Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry, Molecular and Cellular Proteomics, 4 (4) 419-434
• Venables, W.N. and Ripley, B.D. (2003) Modern applied statistics with S, Springer 4th ed.
• Bruce, A., and Gao, H.Y. (2006) Applied wavelet analysis with S-PLUS, Springer 1st Ed.

Ingileif B. Hallgrimsdottir
Title: Lessons from MolPAGE on analysis of proteomics and metabonomics data on the same samples
Recommended Reading
• Coombes, K. R. et al., (2005), Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform,Proteomics 5,4107-4117.
• Morris, J. S. et al., (2005), Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum, Bioinformatics, 21 (9) 1764-1775
• Listgarten, J. and Emili., A. (2005) Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry, Molecular and Cellular Proteomics, 4 (4) 419-434
• Venables, W.N. and Ripley, B.D. (2003) Modern applied statistics with S, Springer 4th ed.
• Bruce, A., and Gao, H.Y. (2006) Applied wavelet analysis with S-PLUS, Springer 1st Ed.