title: Testing for presence of known and unknown molecules in imaging mass spectrometry.
abstract: BACKGROUND
  Imaging mass spectrometry has emerged in the past decade as a label-free, spatially resolved and multi-purpose bioanalytical technique for direct analysis of biological samples. However, solving two everyday data analysis problems still requires expert judgment: (i) the detection of unknown molecules and (ii) the testing for presence of known molecules.
  
  
  RESULTS
  We developed a measure of spatial chaos of a molecular image corresponding to a mass-to-charge value, which is a proxy for the molecular presence, and developed methods solving considered problems. The statistical evaluation was performed on a dataset from a rat brain section with test sets of molecular images selected by an expert. The measure of spatial chaos has shown high agreement with expert judges. The method for detection of unknown molecules allowed us to find structured molecular images corresponding to spectral peaks of any low intensity. The test for presence applied to a list of endogenous peptides ranked them according to the proposed measure of their presence in the sample.
  
  
  BACKGROUND
  The source code and test sets of mass-to-charge images are available at http://www.math.uni-bremen.de/∼theodore.
  
  
  BACKGROUND
  Supplementary materials are available at Bioinformatics online.
  
  
  BACKGROUND
  theodore@uni-bremen.de.
authors.affiliation: Center for Industrial Mathematics, University of Bremen, 28359 Bremen, Germany. theodore@uni-bremen.de
authors.forename: Theodore
authors.initials: T
authors.lastname: Alexandrov
authors.forename: Andreas
authors.initials: A
authors.lastname: Bartels
mesh_terms: D000818:Animals; D001923:Brain Chemistry; D007091:Image Processing, Computer-Assisted; D010455:Peptides / Q000032:analysis; D051381:Rats; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
chemical_list: D010455:Peptides