title: Chemometric analysis of MALDI mass spectrometric images of three-dimensional cell culture systems.
abstract: As imaging mass spectrometry (IMS) has grown in popularity in recent years, the applications of this technique have become increasingly diverse. Currently there is a need for sophisticated data processing strategies that maximize the information gained from large IMS data sets. Traditional two-dimensional heat maps of single ions generated in IMS experiments lack analytical detail, yet manual analysis of multiple peaks across hundreds of pixels within an entire image is time-consuming, tedious and subjective. Here, various chemometric methods were used to analyze data sets obtained by matrix-assisted laser desorption/ionization (MALDI) IMS of multicellular spheroids. HT-29 colon carcinoma multicellular spheroids are an excellentin vitromodel system that mimic the three dimensional morphology of tumorsin vivo. These data are especially challenging to process because, while different microenvironments exist, the cells are clonal which can result in strong similarities in the mass spectral profiles within the image. In this proof-of-concept study, a combination of principal component analysis (PCA), clustering methods, and linear discriminant analysis was used to identify unique spectral features present in spatially heterogeneous locations within the image. Overall, the application of these exploratory data analysis tools allowed for the isolation and detection of proteomic changes within IMS data sets in an easy, rapid, and unsupervised manner. Furthermore, a simplified, non-mathematical theoretical introduction to the techniques is provided in addition to full command routines within the MATLAB programming environment, allowing others to easily utilize and adapt this approach.
authors.affiliation: Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN.
authors.forename: Eric M
authors.initials: EM
authors.lastname: Weaver
authors.affiliation: Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN.
authors.forename: Amanda B
authors.initials: AB
authors.lastname: Hummon
authors.affiliation: Chemistry Department, Roanoke College, Salem, VA.
authors.forename: Richard B
authors.initials: RB
authors.lastname: Keithley
keywords: 3D cell culture; MALDI imaging; MATLAB; Principal Component Analysis; chemometrics