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NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing
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Section: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.
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This article has been cited by 10 ACS Journal articles (5 most recent appear below).
De Novo Sequencing of Tryptic Peptides Derived from Deinococcus radiodurans Ribosomal Proteins Using 157 nm Photodissociation MALDI TOF/TOF Mass Spectrometry
Liangyi Zhang and James P. ReillyJournal of Proteome Research2010 9 (6), 3025-3034De Novo Sequencing of Tryptic Peptides Derived from Deinococcus radiodurans Ribosomal Proteins Using 157 nm Photodissociation MALDI TOF/TOF Mass Spectrometry
Liangyi Zhang and James P. ReillyJournal of Proteome Research2010 9 (6), 3025-3034Vacuum ultraviolet photodissociation of peptide ions in a matrix assisted laser desorption ionization (MALDI) tandem time-of-flight (TOF) mass spectrometer is used to characterize peptide mixtures derived from Deinococcus radiodurans ribosomal proteins. ...
pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra
Hao Chi, Rui-Xiang Sun, Bing Yang, Chun-Qing Song, Le-Heng Wang, Chao Liu, Yan Fu, Zuo-Fei Yuan, Hai-Peng Wang, Si-Min He and Meng-Qiu DongJournal of Proteome Research2010 9 (5), 2713-2724pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra
Hao Chi, Rui-Xiang Sun, Bing Yang, Chun-Qing Song, Le-Heng Wang, Chao Liu, Yan Fu, Zuo-Fei Yuan, Hai-Peng Wang, Si-Min He and Meng-Qiu DongJournal of Proteome Research2010 9 (5), 2713-2724De novo peptide sequencing has improved remarkably in the past decade as a result of better instruments and computational algorithms. However, de novo sequencing can correctly interpret only
30% of high- and medium-quality spectra generated by collision-...
Peptide de Novo Sequencing Using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer
Liangyi Zhang and James P. ReillyAnalytical Chemistry2010 82 (3), 898-908Peptide de Novo Sequencing Using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer
Liangyi Zhang and James P. ReillyAnalytical Chemistry2010 82 (3), 898-908It has previously been shown that photodissociation of tryptic peptide ions with 157 nm light in a matrix-assisted laser desorption/ionization (MALDI) tandem time-of-flight (TOF) mass spectrometer generates an abundance of x-type ions. A peptide de novo ...
A Ranking-Based Scoring Function for Peptide−Spectrum Matches
Ari M. FrankJournal of Proteome Research2009 8 (5), 2241-2252A Ranking-Based Scoring Function for Peptide−Spectrum Matches
Ari M. FrankJournal of Proteome Research2009 8 (5), 2241-2252We present a novel approach to scoring of peptide−spectrum matches. We use discriminative boosting-based algorithms that are able to harnesses the large volume of MS/MS data presently available to train more accurate scoring models. Our new method ...
DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring
David L. Tabb, Ze-Qiang Ma, Daniel B. Martin, Amy-Joan L. Ham and Matthew C. ChambersJournal of Proteome Research2008 7 (9), 3838-3846DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring
David L. Tabb, Ze-Qiang Ma, Daniel B. Martin, Amy-Joan L. Ham and Matthew C. ChambersJournal of Proteome Research2008 7 (9), 3838-3846In shotgun proteomics, tandem mass spectra of peptides are typically identified through database search algorithms such as Sequest. We have developed DirecTag, an open-source algorithm to infer partial sequence tags directly from observed fragment ions. ...
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- Published In Issue November 15, 2005
- Received for review May 20, 2005. Accepted September 2, 2005.
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