title: NovoHMM: a hidden Markov model for de novo peptide sequencing.
abstract: De novo sequencing of peptides poses one of the most challenging tasks in data analysis for proteome research. In this paper, a generative hidden Markov model (HMM) of mass spectra for de novo peptide sequencing which constitutes a novel view on how to solve this problem in a Bayesian framework is proposed. Further extensions of the model structure to a graphical model and a factorial HMM to substantially improve the peptide identification results are demonstrated. Inference with the graphical model for de novo peptide sequencing estimates posterior probabilities for amino acids rather than scores for single symbols in the sequence. Our model outperforms state-of-the-art methods for de novo peptide sequencing on a large test set of spectra.
authors.affiliation: Institute of Computational Science, Institute of Plant Sciences, ETH Zurich, Switzerland.
authors.forename: Bernd
authors.initials: B
authors.lastname: Fischer
authors.forename: Volker
authors.initials: V
authors.lastname: Roth
authors.forename: Franz
authors.initials: F
authors.lastname: Roos
authors.forename: Jonas
authors.initials: J
authors.lastname: Grossmann
authors.forename: Sacha
authors.initials: S
authors.lastname: Baginsky
authors.forename: Peter
authors.initials: P
authors.lastname: Widmayer
authors.forename: Wilhelm
authors.initials: W
authors.lastname: Gruissem
authors.forename: Joachim M
authors.initials: JM
authors.lastname: Buhmann
mesh_terms: D000595:Amino Acid Sequence; D013058:Mass Spectrometry; D008954:Models, Biological; D008970:Molecular Weight; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011336:Probability; D017510:Protein Folding
chemical_list: D010455:Peptides