title: Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy.
abstract: BACKGROUND
  The bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics nowadays for identifying proteins from a sequence database. De novo sequencing software is also available for sequencing novel peptides with relatively short sequence lengths. However, automated sequencing of novel proteins from MS/MS remains a challenging problem.
  
  
  RESULTS
  Very often, although the target protein is novel, it has a homologous protein included in a known database. When this happens, we propose a novel algorithm and automated software tool, named Champs, for sequencing the complete protein from MS/MS data of a few enzymatic digestions of the purified protein. Validation with two standard proteins showed that our automated method yields >99% sequence coverage and 100% sequence accuracy on these two proteins. Our method is useful to sequence novel proteins or 're-sequence' a protein that has mutations comparing with the database protein sequence.
authors.affiliation: David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Canada.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Liu
authors.forename: Yonghua
authors.initials: Y
authors.lastname: Han
authors.forename: Denis
authors.initials: D
authors.lastname: Yuen
authors.forename: Bin
authors.initials: B
authors.lastname: Ma
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001331:Automation / Q000379:methods*; D002417:Cattle; D002645:Chickens; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D009113:Muramidase / Q000737:chemistry; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012710:Serum Albumin, Bovine / Q000737:chemistry
chemical_list: D012710:Serum Albumin, Bovine; D009113:Muramidase