title: Spectral probabilities of top-down tandem mass spectra.
abstract: BACKGROUND
  In mass spectrometry-based proteomics, the statistical significance of a peptide-spectrum or protein-spectrum match is an important indicator of the correctness of the peptide or protein identification. In bottom-up mass spectrometry, probabilistic models, such as the generating function method, have been successfully applied to compute the statistical significance of peptide-spectrum matches for short peptides containing no post-translational modifications. As top-down mass spectrometry, which often identifies intact proteins with post-translational modifications, becomes available in many laboratories, the estimation of statistical significance of top-down protein identification results has come into great demand.
  
  
  RESULTS
  In this paper, we study an extended generating function method for accurately computing the statistical significance of protein-spectrum matches with post-translational modifications. Experiments show that the extended generating function method achieves high accuracy in computing spectral probabilities and false discovery rates.
  
  
  CONCLUSIONS
  The extended generating function method is a non-trivial extension of the generating function method for bottom-up mass spectrometry. It can be used to choose the correct protein-spectrum match from several candidate protein-spectrum matches for a spectrum, as well as separate correct protein-spectrum matches from incorrect ones identified from a large number of tandem mass spectra.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Liu
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Segar
authors.forename: Shuai Cheng
authors.initials: SC
authors.lastname: Li
authors.forename: Sangtae
authors.initials: S
authors.lastname: Kim
mesh_terms: D019295:Computational Biology / Q000379:methods*; D015233:Models, Statistical; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000378:metabolism*; D040901:Proteomics; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D011506:Proteins