Abstract
The identification of new diagnostic, prognostic, or theranostics biomarkers is one of the main aims of clinical research. Technologies like mass spectrometry (MS) focus on the discovery of proteins as biomarkers and are commonly being used for this purpose. Mass spectrometry consists in the separation by gas of charged molecules, based on their mass-over-charge. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) first involves a separation by liquid chromatography (LC) followed by mass spectrometry in the MS and MS/MS modes.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Sandin, M., Chawade, A., & Levander, F. (2015). Is label-free lc-ms/ms ready for biomarker discovery? Proteomics Clinical Applications, 9, 289–294.
Oberg, A. L., & Vitek, O. (2009). Statistical design of quantitative mass spectrometry-based proteomic experiments. Journal of Proteome Research, 8(5), 2144–2156.
Ma, K., Vitek, O., & Nesvizhskii, A. I. (2012). A statistical model-building perspective to identification of ms/ms spectra with peptideprophet. BMC Bioinformatics, 13(Suppl 16), S1.
Deutsch, E. W., Mendoza, L., Shteynberg, D., Farrah, T., Lam, H., Tasman, N., et al. (2010). A guided tour of the trans-proteomic pipeline. Proteomics, 10(6), 1150–1159.
Shteynberg, D., Deutsch, E. W., Lam, H., Eng, J. K., Sun, Z., Tasman, N., et al. (2011) iProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Molecular and Cellular Proteomics, 10, M111.007690.
Nesvizhskii, A. I., Keller, A., Kolker, E., & Aebersold, R. (2003). A statistical model for identifying proteins by tandem mass spectrometry. Analytical Chemistry, 75(17), 4646–4658.
Karpievitch, Y., Dabney, A., & Smith, R. (2012). Normalization and missing value imputation for label-free lc-ms analysis. BMC Bioinformatics, 13(Suppl 16), S5.
Lai, X., Wang, L., Tang, H., & Witzmann, F. A. (2011). A novel alignment method and multiple filters for exclusion of unqualified peptides to enhance label-free quantification using peptide intensity in lc-ms/ms. Journal of Proteome Research, 10(10), 4799–4812.
Lange, E., Tautenhahn, R., Neumann, S., & Gröpl, C. (2008). Critical assessment of alignment procedures for lc-ms proteomics and metabolomics measurements. BMC Bioinformatics, 9, 375.
Smith, R., Ventura, D., & Prince, J. T. (2015). Lc-ms alignment in theory and practice: A comprehensive algorithmic review. Briefings in Bioinformatics, 16(1), 104–117.
Monroe, M. E., Shaw, J. L., Daly, D. S., Adkins, J. N., & Smith, R. D. (2008). Masic: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected lc-ms(/ms) features. Computational Biology and Chemistry, 32(3), 215–217.
Valot, B., Langella, O., Nano, E., & Zivy, M. (2011). Masschroq: A versatile tool for mass spectrometry quantification. Proteomics, 11(17), 3572–3577.
Polpitiya, A. D., Qian, W.-J., & Jaitly, N. (2008). Dante: A statistical tool for quantitative analysis of - omics data. Bioinformatics, 24, 1556–1558.
Clough, T., Key, M., Ott, I., Ragg, S., Schadow, G., & Vitek, O. (2009). Protein quantification in label-free lc-ms experiments. Journal of Proteome Research, 8(11), 5275–5284.
Choi, M., Chang, C.-Y., & Vitek, O. (2014). MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments. R package version 2.4.0.
Matzke, M., Brown, J. N., Gritsenko, M. A., Metz, T. O., Pounds, J. G., Rodland, K. D., et al. (2013). A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free lc-ms proteomics experiments. Proteomics, 13(3–4), 493–503.
Callister, S. J., Barry, R. C., Adkins, J. N., Johnson, E. T., Qian, W.-J., Webb-Robertson, B.-J.M., et al. (2006) Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. Journal of Proteome Research, 5(2), 277–286.
Bolstad, B. M., Irizarry, R. A., Astrand, M., & Speed, T. P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19(2), 185–193.
Karpievitch, Y. V., Taverner, T., Adkins, J. N., Callister, S. J., Anderson, G. A., Smith, R. D., et al. (2009) Normalization of peak intensities in bottom-up ms-based proteomics using singular value decomposition. Bioinformatics, 25(19), 2573–2580.
Karpievitch, Y. V., Nikolic, S. B., Wilson, R., Sharman, J. E., & Edwards, L. M. (2014) Metabolomics data normalization with eigenms. PLoS One, 9(12), e116221.
Leek, J. T., & Storey, J. D. (2007). Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet, 3(9), e161.
Chawade, A., Alexandersson, E., & Levander, F. (2014). Normalyzer: A tool for rapid evaluation of normalization methods for omics data sets. Journal of Proteome Research, 13(6), 3114–3120.
Lai, X., Wang, L., & Witzmann, F.A. (2013). Issues and applications in label-free quantitative mass spectrometry. International Journal of Proteomics, 2013, Article ID 756039.
Chawade, A., Sandin, M., Teleman, J. N., Malmströ, J., & Levander, F. (2015). Data processing has major impact on the outcome of quantitative label-free lc-ms analysis. Journal of Proteome Research, 14(2), 676–687.
Zou, H., Hastie, T., & Tibshirani, R. (2004). Sparse principal component analysis. Journal of Computational and Graphical Statistics, 15, 2006.
Benjamini, Y., & Hochberg, Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B, 57(1), 289–300.
Wold, H. (2005). In S. Kots & N.L. Johnson (Eds.), Partial least squares. New York: Wiley.
Boulesteix, A.-L., & Strimmer, K. (2007). Partial least squares: A versatile tool for the analysis of high-dimensional genomic data. Briefings in Bioinformatics, 8(1), 32–44.
Tibshirani, R. (1996). Regression shrinkage, selection via the lasso. Journal of the Royal Statistical Society, Series B, 58, 267–288.
Hoerl, A., & Kennard, W. (1970). Ridge regression: Applications to nonorthogonal problems. Technometrics, 12(1), 69–82.
Zou, H., & Hastie, T. (2005). Regularization and variable selection via the elastic net. Journal of the Royal Statistical Society, Series B: Statistical Methodology, 67(2), 301–320.
Truntzer, C., Mostacci, E., Jeannin, A., Petit, J. M., Ducoroy, P., & Cardot, H. (2014). Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data. BMC Bioinformatics, 15(385), 1–12.
Chun, H., & Keles, S. (2010). Sparse partial least squares regression for simultaneous dimension reduction and variable selection. Journal of the Royal Statistical Society, Series B: Statistical Methodology, 72, 3–25.
Clough, T., Thaminy, S., Ragg, S., Aebersold, R., & Vitek, O. (2012). Statistical protein quantification and significance analysis in label-free lc-ms experiments with complex designs. BMC Bioinformatics, 13(Suppl 16), S6.
Truntzer, C., Maucort-Boulch, D., & Roy, P. (2013). Impact of the selection mechanism in the identification and validation of new “omic” biomarkers. Journal of Proteomics and Bioinformatics, 6(8), 164–170.
Lopes, C. T., Franz, M., Kazi, F., Donaldson, S. L., Morris, Q., & Bader, G. D. (2010) Cytoscape web: an interactive web-based network browser. Bioinformatics, 26(18), 2347–2348.
Acknowledgements
We wish to thank the members of the CLIPP Platform (University of Burgundy) for their contribution, and most particularly Géraldine Lucchi and Delphine Pecqueur, who read the article thoroughly. We also wish to thank the “Centre de Langues” (University of Burgundy) for editing the manuscript.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Truntzer, C., Ducoroy, P. (2017). Statistical Approach for Biomarker Discovery Using Label-Free LC-MS Data: An Overview. In: Datta, S., Mertens, B. (eds) Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry. Frontiers in Probability and the Statistical Sciences. Springer, Cham. https://doi.org/10.1007/978-3-319-45809-0_10
Download citation
DOI: https://doi.org/10.1007/978-3-319-45809-0_10
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-45807-6
Online ISBN: 978-3-319-45809-0
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)