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Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification

By Aaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael J. MacCoss and William Stafford Noble

Abstract

Motivation: Tandem mass spectrometry (MS/MS) is an indispensable technology for identification of proteins from complex mixtures. Proteins are digested to peptides that are then identified by their fragmentation patterns in the mass spectrometer. Thus, at its core, MS/MS protein identification relies on the relative predictability of peptide fragmentation. Unfortunately, peptide fragmentation is complex and not fully understood, and what is understood is not always exploited by peptide identification algorithms

Topics: Ismb 2008 Conference Proceedings 19–23 July 2008, Toronto
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:2665034
Provided by: PubMed Central
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    Citations

    1. (2007). A semi-supervised machine learning technique for peptide identification from shotgun proteomics datasets.
    2. (1994). An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.
    3. (2001). Analysis of proteins and proteomes by mass spectrometry.
    4. (2008). Assigning significance to peptides identified by tandem mass spectrometry using decoy databases.
    5. (1999). De novo peptide sequencing via tandem mass spectrometry.
    6. (2004). Electron-capture dissociation tandem mass spectrometry.
    7. (2004). Fragmentation pathways of protonated peptides.
    8. (2005). Graphical model architectures for speech recognition.
    9. (2003). Gutentag: high-throughput sequence tagging via an empirically derived fragmentation model.
    10. (2007). High speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics datasets using high resolution mass spectrometry.
    11. (2007). Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions.
    12. (2004). Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides.
    13. (1996). Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: evidence for the mobile proton model.
    14. (2005). InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra.
    15. (2004). Intensity-based protein identification by machine learning from a library of tandem mass spectra.
    16. (2003). Intensity-based statistical scorer for tandem mass spectrometry.
    17. (2001). Large-scale analysis of the yeast proteome by multidimensional protein identification technology.
    18. (1998). Mass spectrometry and the age of the proteome.
    19. (2003). Matrix2png: a utility for visualizing matrix data.
    20. (1995). on learning with Bayesian Networks.
    21. (2004). Open mass spectrometry search algorithm.
    22. (2005). PepHMM: a hidden Markov model based scoring function for mass spectrometry database search.
    23. (2005). Pepnovo: de novo peptide sequencing via probabilistic network modeling.
    24. (2004). Prediction of low-energy collision-induced dissociation spectra of peptides.
    25. (2002). ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data.
    26. (2000). Protein sequencing and identification using tandem mass spectrometry. Wiley-Interscience,
    27. (2002). Radars, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database.
    28. (2008). Rapid and accurate peptide identification from tandem mass spectra.
    29. (2001). SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database.
    30. (1997). Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid commun.
    31. (2003). Statistical significance for genome-wide studies.
    32. (2007). The utility of ETD mass spectrometry in proteomic analysis.

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