Peptide detectability following ESI mass spectrometry: Prediction using genetic programming.

David C. Wedge, Simon J. Gaskell, Simon J. Hubbard, Douglas B. Kell, King Wai Lau, Claire Eyers

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Abstract

    The accurate quantification of proteins is important in several areas of cell biology, biotechnology and medicine. Both relative and absolute quantification of proteins is often determined following mass spectrometric analysis of one or more of their constituent peptides. However, in order for quantification to be successful, it is important that the experimenter knows which peptides are readily detectable under the mass spectrometric conditions used for analysis. In this paper, genetic programming is used to develop a function which predicts the detectability of peptides from their calculated physico-chemical properties. Classification is carried out in two stages: the selection of a good classifier using the AUROC objective function and the setting of an appropriate threshold. This allows the user to select the balance point between conflicting priorities in an intuitive way. The success of this method is found to be highly dependent on the initial selection of input parameters. The use of brood recombination and a modified version of the multi-objective FOCUS method are also investigated. While neither has a significant effect on predictive accuracy, the use of the FOCUS method leads to considerably more compact solutions. Copyright 2007 ACM.
    Original languageEnglish
    Title of host publicationProceedings of GECCO 2007: Genetic and Evolutionary Computation Conference|Proc. Gen. Evol. Comput. Conf.
    Place of PublicationNew York
    PublisherAssociation for Computing Machinery
    Pages2219-2225
    Number of pages6
    ISBN (Print)1595936971, 9781595936974
    DOIs
    Publication statusPublished - 2007
    Event9th Annual Genetic and Evolutionary Computation Conference, GECCO 2007 - London
    Duration: 1 Jul 2007 → …
    http://dblp.uni-trier.de/db/conf/gecco/gecco2007.html#BrankeLS07http://dblp.uni-trier.de/rec/bibtex/conf/gecco/BrankeLS07.xmlhttp://dblp.uni-trier.de/rec/bibtex/conf/gecco/BrankeLS07

    Conference

    Conference9th Annual Genetic and Evolutionary Computation Conference, GECCO 2007
    CityLondon
    Period1/07/07 → …
    Internet address

    Keywords

    • AUROC
    • Classification
    • Genetic programming
    • Input selection
    • Mass spectrometry
    • Proteomics

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