title: De novo peptide sequencing via tandem mass spectrometry.
abstract: Peptide sequencing via tandem mass spectrometry (MS/MS) is one of the most powerful tools in proteomics for identifying proteins. Because complete genome sequences are accumulating rapidly, the recent trend in interpretation of MS/MS spectra has been database search. However, de novo MS/MS spectral interpretation remains an open problem typically involving manual interpretation by expert mass spectrometrists. We have developed a new algorithm, SHERENGA, for de novo interpretation that automatically learns fragment ion types and intensity thresholds from a collection of test spectra generated from any type of mass spectrometer. The test data are used to construct optimal path scoring in the graph representations of MS/MS spectra. A ranked list of high scoring paths corresponds to potential peptide sequences. SHERENGA is most useful for interpreting sequences of peptides resulting from unknown proteins and for validating the results of database search algorithms in fully automated, high-throughput peptide sequencing.
authors.affiliation: Millennium Pharmaceuticals, Cambridge, Massachusetts 02139, USA. dancik@mpi.com
authors.forename: V
authors.initials: V
authors.lastname: Dancík
authors.forename: T A
authors.initials: TA
authors.lastname: Addona
authors.forename: K R
authors.initials: KR
authors.lastname: Clauser
authors.forename: J E
authors.initials: JE
authors.lastname: Vath
authors.forename: P A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D016208:Databases, Factual; D005069:Evaluation Studies as Topic; D013058:Mass Spectrometry / Q000379:methods* / Q000706:statistics & numerical data; D010455:Peptides / Q000737:chemistry*; D017421:Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data
chemical_list: D010455:Peptides