Abstract
In shotgun proteomics, more abundant peptides are selected for MS/MS fragmentation leading to sequence assignment and their quantitative abundance is computed from peak area of the extracted ion chromatogram. This analysis framework is called data dependent acquisition (DDA). However, the bias towards abundant peptides limits reproducible extraction of peptide signals for a large proportion of the proteome. Recent advances in next generation mass spectrometers enabled implementation of an alternative approach called data independent acquisition (DIA), which improves data quality in terms of dynamic range, measurement precision, and more importantly, reproducible detection. In this chapter, we review the process of generating quantitative proteomics data with DIA, and present a computational tool mapDIA designed for data processing and statistical analysis of the DIA proteomics data. Using an example of renal cancer data set, we demonstrate that fragment intensity data from DIA provide a reliable repeated measure of peptide abundance after careful filtering, and direct modeling of the hierarchical data (protein → peptide → fragment) improves the detection of differentially expressed proteins compared to the analysis using protein intensity data derived by summation of fragment intensities.
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Besag, J. (1986). On the statistical analysis of dirty pictures. Journal of the Royal Statistical Society: Series B, 48, 259–302.
Choi, H., Kim, S., Fermin, D., Tsou, C. C., & Nesvizhskii, A. I. (2015). QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics. Journal of Proteomics, 129, 121–126.
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.
Collins, B. C., Gillet, L. C., Rosenberger, G., Röst, H. L., Vichalkovski, A., Gstaiger, M., et al. (2013). Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system. Nature Methods, 10(12), 1246–1253.
Craig, R., & Beavis, R. C. (2003). A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Communications in Mass Spectrometry, 17, 2310–2316.
Egertson, J. D., Kuehn, A., Merrihew, G. E., Bateman, N. W., MacLean, B. X., Ting, Y. S., et al. (2013). Multiplexed MS/MS for improved data-independent acquisition. Nature Methods, 10, 744–746.
Gillet, L. C., Navarro, P., Tate, S., Röst, H. L., Selevsek, N., Reiter, L., et al. (2012). Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis. Molecular & Cellular Proteomics, 11(6), O111.016717.
Guo, T., Kouvonen, P., Koh, C. C., Gillet, L. C., Wolski, W., Röst, H. L., et al. (2015). Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nature Medicine, 21(4), 407–413.
Karpievitch, Y., Stanley, J., Taverner, T., Huang, J., Adkins, J. N., Ansong, C., et al. (2009). A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinformatics, 25(16), 2028–2034.
Lambert, J. P., Ivosev, G., Couzens, A. L., Larsen, B., Taipale, M., Lin, Z. Y., et al. (2013). Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition. Nature Methods, 10(12), 1239–1245.
MacLean, B. X., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., et al. (2010). Skyline: An open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics, 26(7), 966–968.
Newton, M. A., Noueiry, A., Sarkar, D., & Ahlquist, P. (2004). Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics, 5(2), 155–176.
Panchaud, A., Scherl, A., Shaffer, S. A., von Haller, P. D., Kulasekara, H. D., Miller, S. I., et al. (2009). PAcIFIC: How to dive deeper into the proteomics ocean. Analytical Chemistry, 81(15), 6481–6488.
Prakash, A., Peterman, S., Ahmad, S., Sarracino, D., Frewen, B., Vogelsang, M., et al. (2013). Hybrid data acquisition and processing strategies with increased throughput and selectivity: pSMART analysis for global qualitative and quantitative analysis. Journal of Proteome Research, 12, 5415–5430.
Röst, H. L., Rosenberger, G., Navarro, P., Gillet, L., Miladinović, S. M., Schubert, O. T., et al. (2014). Openswath enables automated, targeted analysis of data-independent acquisition MS data. Nature Biotechnology, 32(3), 219–223.
Schubert, O. T., Gillet, L. C., Collins, B. C., Navarro, P., Rosenberger, G., Wolski, W., et al. (2015). Building high-quality assay libraries for targeted analysis of SWATH MS data. Nature Protocols, 10(3), 426–441.
Silva, J. C., Gorenstein, M. V., Li, G. Z., Vissers, J. P. C., & Geromanos, S. J. (2006). Absolute quantification of proteins by LCMSE: A virtue of parallel ms acquisition. Molecular & Cellular Proteomics, 5, 144–156.
Steen, H., & Mann, M. (2004). The abc’s (and xyz’s) of peptide sequencing. Nature Reviews Molecular Cell Biology, 5(9), 699–711.
Teo, G. S., Kim, S., Tsou, C.-C., Gingras, A.-C., Nesvizhskii, A. I., & Choi, H. (2015). mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry. Journal of Proteomics, 129, 108–120.
Tsou, C.-C., Avtonomov, D., Larsen, B., Tucholska, M., Choi, H., Gingras, A.-C., et al. (2015). DIA-Umpire: Comprehensive computational framework for data independent acquisition proteomics. Nature Methods, 12(3), 258–264.
Venable, J. D., Dong, M. Q., Wohlschlegel, J., Dillin, A., & Yatesm, J. R. (2004). Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nature Methods, 1(1), 39–45.
Wei, Z., & Li, H. (2007). A Markov random field model for network-based analysis of genomic data. Bioinformatics, 23(12), 1537–1544.
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Chen, G., Teo, G.S., Teo, G.C., Choi, H. (2017). Model-Based Analysis of Quantitative Proteomics Data with Data Independent Acquisition Mass Spectrometry. 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_7
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DOI: https://doi.org/10.1007/978-3-319-45809-0_7
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