A mass spectrometry imaging toolbox for statistical analysis. Cardinal is an R package that implements statistical and computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.
A vendor-neutral interface built on the Matlab platform designed to view and perform data analysis of Mass Spectrometry Imaging (MSI) data. A standalone version of MSiReader for which Matlab is not required is also provided. People who are unfamiliar with the Matlab language will have little difficulty navigating the user friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.
Permits users extract text-plain spectra from binary Thermo Scientific RAW files. pXtract is a portable application that provides a user interface. It includes options to export a particular type of activation spectra of tandem mass-spectrometry (MS/MS), to export all of the outputs in a choosen directory, to specify whether the exported spectra should be centroided or not.
Presents an improved data analysis pipeline based on a new peak picking method for exploring imaging mass spectrometry data. EXIMS consists of five consecutive main steps: where the first step involves spectra preprocessing. Then, Sliding Window Normalization (SWN) is used to normalize the spectra and limit the influence of high intensity peaks. Third, image de-noising and contrast enhancement are used to improve the visualization of intensity images. Fourth, peak picking is performed by processing the individual intensity images. Finally, intensity images are clustered using the fuzzy cmeans clustering algorithm.