title: A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data.
abstract: BACKGROUND
  Mass spectrometry (MS)-based proteomics is one of the most commonly used research techniques for identifying and characterizing proteins in biological and medical research. The identification of a protein is the critical first step in elucidating its biological function. Successful protein identification depends on various interrelated factors, including effective analysis of MS data generated in a proteomic experiment. This analysis comprises several stages, often combined in a pipeline or workflow. The first component of the analysis is known as spectra pre-processing. In this component, the raw data generated by the mass spectrometer is processed to eliminate noise and identify the mass-to-charge ratio (m/z) and intensity for the peaks in the spectrum corresponding to the presence of certain peptides or peptide fragments. Since all downstream analyses depend on the pre-processed data, effective pre-processing is critical to protein identification and characterization. There is a critical need for more robust pre-processing algorithms that perform well on tandem mass spectra under a variety of different conditions and can be easily integrated into sophisticated data analysis pipelines for practical wet-lab applications.
  
  
  RESULTS
  We have developed a new pre-processing algorithm. Based on wavelet theory, our method uses a dynamic peak model to identify peaks. It is designed to be easily integrated into a complete proteomic analysis workflow. We compared the method with other available algorithms using a reference library of raw MS and tandem MS spectra with known protein composition information. Our pre-processing algorithm results in the identification of significantly more peptides and proteins in the downstream analysis for a given false discovery rate.
  
  
  BACKGROUND
  Software available at: http://www.maths.usyd.edu.au/u/penghao/index.html.
authors.affiliation: School of Mathematics and Statistics, University of Sydney, Sydney, Australia. penghao.wang@sydney.edu.au
authors.forename: Penghao
authors.initials: P
authors.lastname: Wang
authors.forename: Pengyi
authors.initials: P
authors.lastname: Yang
authors.forename: Jonathan
authors.initials: J
authors.lastname: Arthur
authors.forename: Jean Yee Hwa
authors.initials: JY
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D015233:Models, Statistical; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D011506:Proteins