Abstract
Mass spectrometry imaging produces large numbers of spectra that need to be efficiently stored, processed, and analyzed. In this chapter, we describe the protocol and methods for data processing, visualization, and statistical analysis, with related techniques and tools available presented. Examples are given with data collected for a 3D MS imaging of a mouse brain and 2D MS imaging of human bladder tissues.
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References
Jones EA, Deininger SO, Hogendoorn PCW, Deelder AM, McDonnell LA (2012) Imaging mass spectrometry statistical analysis. J Proteomics 75(16):4962–4989
Eberlin LS, Norton I, Dill AL, Golby AJ, Ligon KL, Santagata S, Cooks RG, Agar NYR (2012) Classifying human brain tumors by lipid imaging with mass spectrometry. Cancer Res 72(3):645–654
Masterson TA, Dill AL, Eberlin LS, Mattarozzi M, Cheng L, Beck SDW, Bianchi F, Cooks RG (2011) Distinctive glycerophospholipid profiles of human seminoma and adjacent normal tissues by desorption electrospray ionization imaging mass spectrometry. J Am Soc Mass Spectrom 22(8):1326–1333
Dill AL, Eberlin LS, Zheng C, Costa AB, Ifa DR, Cheng LA, Masterson TA, Koch MO, Vitek O, Cooks RG (2010) Multivariate statistical differentiation of renal cell carcinomas based on lipidomic analysis by ambient ionization imaging mass spectrometry. Anal Bioanal Chem 398(7–8):2969–2978
Dill AL, Eberlin LS, Costa AB, Zheng C, Ifa DR, Cheng LA, Masterson TA, Koch MO, Vitek O, Cooks RG (2011) Multivariate statistical identification of human bladder carcinomas using ambient ionization imaging mass spectrometry. Chemistry 17(10):2897–2902
Eberlin LS, Ifa DR, Wu C, Cooks RG (2010) Three-dimensional visualization of mouse brain by lipid analysis using ambient ionization mass spectrometry. Angew Chem Int Ed Engl 49(5):873–876
Cooks RG, Manicke NE, Dill AL, Ifa DR, Eberlin LS, Costa AB, Wang H, Huang GM, Zheng OY (2011) New ionization methods and miniature mass spectrometers for biomedicine: DESI imaging for cancer diagnostics and paper spray ionization for therapeutic drug monitoring. Faraday Discuss 149:247–267
Xiong XC, Xu W, Eberlin LS, Wiseman JM, Fang X, Jiang Y, Huang ZJ, Zhang YK, Cooks RG, Ouyang Z (2012) Data processing for 3D mass spectrometry imaging. J Am Soc Mass Spectrom 23(6):1147–1156
Liu JJ, Ouyang Z (2013) Mass spectrometry imaging for biomedical applications. Anal Bioanal Chem 405(17):5645–5653
Wiseman JM, Ifa DR, Venter A, Cooks RG (2008) Ambient molecular imaging by desorption electrospray ionization mass spectrometry. Nat Protoc 3(3):517–524
Robichaud G, Garrard KP, Barry JA, Muddiman DC (2013) MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform. J Am Soc Mass Spectrom 24(5):718–721
Smith DF, Kharchenko A, Konijnenburg M, Klinkert I, Pasa-Tolic L, Heeren RMA (2012) Advanced mass calibration and visualization for FT-ICR mass spectrometry imaging. J Am Soc Mass Spectrom 23(11):1865–1872
Jardin-Mathe O, Bonnel D, Franck J, Wisztorski M, Macagno E, Fournier I, Salzet M (2008) MITICS (MALDI Imaging Team Imaging Computing System): a new open source mass spectrometry imaging software. J Proteomics 71(3):332–345
Eberlin LS, Dill AL, Costa AB, Ifa DR, Cheng L, Masterson T, Koch M, Ratliff TL, Cooks RG (2010) Cholesterol sulfate imaging in human prostate cancer tissue by desorption electrospray ionization mass spectrometry. Anal Chem 82(9):3430–3434
Schramm T, Hester A, Klinkert I, Both JP, Heeren RMA, Brunelle A, Laprevote O, Desbenoit N, Robbe MF, Stoeckli M, Spengler B, Rompp A (2012) imzML—a common data format for the flexible exchange and processing of mass spectrometry imaging data. J Proteomics 75(16):5106–5110
Thomas A, Patterson NH, Marcinkiewicz MM, Lazaris A, Metrakos P, Chaurand P (2013) Histology-driven data mining of lipid signatures from multiple imaging mass spectrometry analyses: application to human colorectal cancer liver metastasis biopsies. Anal Chem 85(5):2860–2866
Fonville JM, Carter CL, Pizarro L, Steven RT, Palmer AD, Griffiths RL, Lalor PF, Lindon JC, Nicholson JK, Holmes E, Bunch J (2013) Hyperspectral visualization of mass spectrometry imaging data. Anal Chem 85(3):1415–1423
Pirro V, Eberlin LS, Oliveri P, Cooks RG (2012) Interactive hyperspectral approach for exploring and interpreting DESI-MS images of cancerous and normal tissue sections. Analyst 137(10):2374–2380
Eberlin LS, Liu XH, Ferreira CR, Santagata S, Agar NYR, Cooks RG (2011) Desorption electrospray ionization then MALDI mass spectrometry imaging of lipid and protein distributions in single tissue sections. Anal Chem 83(22):8366–8371
Girod M, Shi YZ, Cheng JX, Cooks RG (2010) Desorption electrospray ionization imaging mass spectrometry of lipids in rat spinal cord. J Am Soc Mass Spectrom 21(7):1177–1189
Girod M, Shi YZ, Cheng JX, Cooks RG (2011) Mapping lipid alterations in traumatically injured rat spinal cord by desorption electrospray ionization imaging mass spectrometry. Anal Chem 83(1):207–215
Wu CP, Ifa DR, Manicke NE, Cooks RG (2010) Molecular imaging of adrenal gland by desorption electrospray ionization mass spectrometry. Analyst 135(1):28–32
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Liu, J., Xiong, X., Ouyang, Z. (2015). Data Processing and Analysis for Mass Spectrometry Imaging. In: He, L. (eds) Mass Spectrometry Imaging of Small Molecules. Methods in Molecular Biology, vol 1203. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1357-2_19
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DOI: https://doi.org/10.1007/978-1-4939-1357-2_19
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