title: A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data.
abstract: BACKGROUND
  Tandem mass spectrometry (MS/MS) is a powerful tool for protein identification. Although great efforts have been made in scoring the correlation between tandem mass spectra and an amino acid sequence database, improvements could be made in three aspects, including characterization ofpeaks in spectra, adoption of effective scoring functions and access to thereliability of matching between peptides and spectra.
  
  
  RESULTS
  A novel scoring function is presented, along with criteria to estimate the performance confidence of the function. Through learning the typesof product ions and the probability of generating them, a hypothetic spectrum was generated for each candidate peptide. Then relative entropy was introduced to measure the similarity between the hypothetic and the observed spectra. Based on the extreme value distribution (EVD) theory, a threshold was chosen to distinguish a true peptide assignment from a random one. Tests on a public MS/MS dataset demonstrated that this method performs better than the well-known SEQUEST.
  
  
  CONCLUSIONS
  A reliable identification of proteins from the spectra promises a more efficient application of tandem mass spectrometry to proteomes with high complexity.
authors.affiliation: Institute of Biophysics, Chinese Academy of Sciences, Beijing, PR China. zhangzhuo77@moon.ibp.ac.cn
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Zhang
authors.forename: Shiwei
authors.initials: S
authors.lastname: Sun
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Suhua
authors.initials: S
authors.lastname: Chang
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Liu
authors.forename: Chungong
authors.initials: C
authors.lastname: Yu
authors.forename: Dongbo
authors.initials: D
authors.lastname: Bu
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods*; D010455:Peptides / Q000032:analysis / Q000737:chemistry* / Q000145:classification; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D010455:Peptides