title: A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise.
abstract: In recent years there has been an increased interest in using protein mass spectroscopy to discriminate diseased from healthy individuals with the aim of discovering molecular markers for disease. A crucial step before any statistical analysis is the pre-processing of the mass spectrometry data. Statistical results are typically strongly affected by the specific pre-processing techniques used. One important pre-processing step is the removal of chemical and instrumental noise from the mass spectra. Wavelet denoising techniques are a standard method for denoising. Existing techniques, however, do not accommodate errors that vary across the mass spectrum, but instead assume a homogeneous error structure. In this paper we propose a novel wavelet denoising approach that deals with heterogeneous errors by incorporating a variance change point detection method in the thresholding procedure. We study our method on real and simulated mass spectrometry data and show that it improves on performances of peak detection methods.
authors.affiliation: Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20852, USA. kwonde@mail.nih.gov
authors.forename: Deukwoo
authors.initials: D
authors.lastname: Kwon
authors.forename: Marina
authors.initials: M
authors.lastname: Vannucci
authors.forename: Joon Jin
authors.initials: JJ
authors.lastname: Song
authors.forename: Jaesik
authors.initials: J
authors.lastname: Jeong
authors.forename: Ruth M
authors.initials: RM
authors.lastname: Pfeiffer
mesh_terms: D001798:Blood Proteins / Q000032:analysis / Q000302:isolation & purification; D005260:Female; D006801:Humans; D010051:Ovarian Neoplasms / Q000097:blood / Q000473:pathology; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*; D015203:Reproducibility of Results; D012815:Signal Processing, Computer-Assisted; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
chemical_list: D001798:Blood Proteins