title: A new scoring function for top-down spectral deconvolution.
abstract: BACKGROUND
  Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isotopomer envelopes from highly charged ions, which may overlap with one another. As a result, spectral deconvolution, which converts a complex top-down mass spectrum into a monoisotopic mass list, is a key step in top-down spectral interpretation.
  
  
  RESULTS
  In this paper, we propose a new scoring function, L-score, for evaluating isotopomer envelopes. By combining L-score with MS-Deconv, a new software tool, MS-Deconv+, was developed for top-down spectral deconvolution. Experimental results showed that MS-Deconv+ outperformed existing software tools in top-down spectral deconvolution.
  
  
  CONCLUSIONS
  L-score shows high discriminative ability in identification of isotopomer envelopes. Using L-score, MS-Deconv+ reports many correct monoisotopic masses missed by other software tools, which are valuable for proteoform identification and characterization.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Kou
authors.forename: Si
authors.initials: S
authors.lastname: Wu
authors.affiliation: Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 535 W, Michigan Street, Indianapolis, IN 46202, USA. xwliu@iupui.edu.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000032:analysis / Q000302:isolation & purification; D002851:Chromatography, High Pressure Liquid; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D016015:Logistic Models; D013058:Mass Spectrometry; D008962:Models, Theoretical; D008970:Molecular Weight; D011506:Proteins / Q000032:analysis*; D012372:ROC Curve; D012486:Salmonella typhimurium / Q000235:genetics / Q000378:metabolism; D012984:Software
chemical_list: D001426:Bacterial Proteins; D011506:Proteins