Data processing and analysis for mass spectrometry imaging.

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.

[1]  R. Cooks,et al.  Desorption electrospray ionization imaging mass spectrometry of lipids in rat spinal cord , 2010, Journal of the American Society for Mass Spectrometry.

[2]  David C Muddiman,et al.  MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform , 2013, Journal of The American Society for Mass Spectrometry.

[3]  R. Cooks,et al.  Desorption electrospray ionization then MALDI mass spectrometry imaging of lipid and protein distributions in single tissue sections. , 2011, Analytical chemistry.

[4]  R. Cooks,et al.  Molecular imaging of adrenal gland by desorption electrospray ionization mass spectrometry. , 2010, The Analyst.

[5]  Luis Pizarro,et al.  Hyperspectral visualization of mass spectrometry imaging data. , 2013, Analytical chemistry.

[6]  Anthony B. Costa,et al.  New ionization methods and miniature mass spectrometers for biomedicine: DESI imaging for cancer diagnostics and paper spray ionization for therapeutic drug monitoring. , 2011, Faraday discussions.

[7]  R. Cooks,et al.  Data Processing for 3D Mass Spectrometry Imaging , 2012, Journal of The American Society for Mass Spectrometry.

[8]  V. Pirro,et al.  Interactive hyperspectral approach for exploring and interpreting DESI-MS images of cancerous and normal tissue sections. , 2012, The Analyst.

[9]  Nathan Heath Patterson,et al.  Histology-driven data mining of lipid signatures from multiple imaging mass spectrometry analyses: application to human colorectal cancer liver metastasis biopsies. , 2013, Analytical chemistry.

[10]  Liang Cheng,et al.  Cholesterol sulfate imaging in human prostate cancer tissue by desorption electrospray ionization mass spectrometry. , 2010, Analytical chemistry.

[11]  R. Cooks,et al.  Distinctive Glycerophospholipid Profiles of Human Seminoma and Adjacent Normal Tissues by Desorption Electrospray Ionization Imaging Mass Spectrometry , 2011, Journal of the American Society for Mass Spectrometry.

[12]  R. Cooks,et al.  Mapping lipid alterations in traumatically injured rat spinal cord by desorption electrospray ionization imaging mass spectrometry. , 2011, Analytical chemistry.

[13]  Maxence Wisztorski,et al.  MITICS (MALDI Imaging Team Imaging Computing System): a new open source mass spectrometry imaging software. , 2008, Journal of proteomics.

[14]  R. Cooks,et al.  Three-dimensional vizualization of mouse brain by lipid analysis using ambient ionization mass spectrometry. , 2010, Angewandte Chemie.

[15]  Z. Ouyang,et al.  Mass spectrometry imaging for biomedical applications , 2013, Analytical and Bioanalytical Chemistry.

[16]  K. Ligon,et al.  Classifying human brain tumors by lipid imaging with mass spectrometry. , 2012, Cancer research.

[17]  Olga Vitek,et al.  Multivariate statistical identification of human bladder carcinomas using ambient ionization imaging mass spectrometry. , 2011, Chemistry.

[18]  R. Cooks,et al.  Ambient molecular imaging by desorption electrospray ionization mass spectrometry , 2008, Nature Protocols.

[19]  Liam A. McDonnell,et al.  Imaging mass spectrometry statistical analysis. , 2012, Journal of proteomics.

[20]  Anthony B. Costa,et al.  Multivariate statistical differentiation of renal cell carcinomas based on lipidomic analysis by ambient ionization imaging mass spectrometry , 2010, Analytical and bioanalytical chemistry.

[21]  Ljiljana Paša-Tolić,et al.  Advanced Mass Calibration and Visualization for FT-ICR Mass Spectrometry Imaging , 2012, Journal of The American Society for Mass Spectrometry.

[22]  Marie-France Robbe,et al.  imzML--a common data format for the flexible exchange and processing of mass spectrometry imaging data. , 2012, Journal of proteomics.