title: Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens.
abstract: BACKGROUND
  Application of mass spectrometry in proteomics is a breakthrough in high-throughput analyses. Early applications have focused on protein expression profiles to differentiate among various types of tissue samples (e.g. normal versus tumor). Here our goal is to use mass spectra to differentiate bacterial species using whole-organism samples. The raw spectra are similar to spectra of tissue samples, raising some of the same statistical issues (e.g. non-uniform baselines and higher noise associated with higher baseline), but are substantially noisier. As a result, new preprocessing procedures are required before these spectra can be used for statistical classification.
  
  
  RESULTS
  In this study, we introduce novel preprocessing steps that can be used with any mass spectra. These comprise a standardization step and a denoising step. The noise level for each spectrum is determined using only data from that spectrum. Only spectral features that exceed a threshold defined by the noise level are subsequently used for classification. Using this approach, we trained the Random Forest program to classify 240 mass spectra into four bacterial types. The method resulted in zero prediction errors in the training samples and in two test datasets having 240 and 300 spectra, respectively.
authors.affiliation: Division of Laboratory Science, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA. gsatten@cdc.gov
authors.forename: Glen A
authors.initials: GA
authors.lastname: Satten
authors.forename: Somnath
authors.initials: S
authors.lastname: Datta
authors.forename: Hercules
authors.initials: H
authors.lastname: Moura
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Woolfitt
authors.forename: Maria da G
authors.initials: Mda G
authors.lastname: Carvalho
authors.forename: George M
authors.initials: GM
authors.lastname: Carlone
authors.forename: Barun K
authors.initials: BK
authors.lastname: De
authors.forename: Antonis
authors.initials: A
authors.lastname: Pavlopoulos
authors.forename: John R
authors.initials: JR
authors.lastname: Barr
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001419:Bacteria / Q000145:classification / Q000302:isolation & purification* / Q000378:metabolism*; D001426:Bacterial Proteins / Q000032:analysis*; D015415:Biomarkers / Q000032:analysis*; D004926:Escherichia coli / Q000302:isolation & purification / Q000378:metabolism; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods* / Q000592:standards
chemical_list: D001426:Bacterial Proteins; D015415:Biomarkers