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    GlycoPep Detector: A tool for assigning mass spectrometry data of N-linked glycopeptides based on their ETD spectra

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    Dessaire_AnalChem_2013.pdf (1.085Mb)
    Issue Date
    2013-05-21
    Author
    Zhu, Zhikai
    Clark, Daniel Forrest
    Go, Eden P.
    Desaire, Heather
    Publisher
    American Chemical Society
    Type
    Article
    Article Version
    Scholarly/refereed, author accepted manuscript
    Rights
    Copyright © 2013 American Chemical Society
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    Abstract
    Electron transfer dissociation (ETD) is commonly used in fragmenting N-linked glycopeptides in their mass spectral analyses to complement collision induced dissociation (CID) experiments. The glycan remains intact through ETD, while the peptide backbone is cleaved, providing the sequence of amino acids for a glycopeptide. Nonetheless, data analysis is a major bottleneck to high throughput glycopeptide identification based on ETD data, due to the complexity and diversity of ETD mass spectra compared to CID counterparts. GlycoPep Detector (GPD) is a web-based tool to address this challenge. It filters out noise peaks that interfere with glycopeptide sequencing, correlates input glycopeptide compositions with the ETD spectra, and assigns a score for each candidate. By considering multiple ion series (c-, z- and y-ions) and scoring them separately, the software gives more weighting to the ion series that matches peaks of high intensity in the spectra. This feature enables the correct glycopeptide to receive a high score while keeping scores of incorrect compositions low. GPD has been utilized to interpret data collected on six model glycoproteins (RNase B, avidin, fetuin, asialofetuin, transferrin and AGP) as well as a clade C HIV envelope glycoprotein, C.97ZA012 gp140ΔCFI. In every assignment made by GPD, the correct glycopeptide composition earns a score that is about two-fold higher than other incorrect glycopeptide candidates (decoys). The software can be accessed at http://glycopro.chem.ku.edu/ZZKHome.php.
    URI
    http://hdl.handle.net/1808/23588
    DOI
    https://doi.org/10.1021/ac400287n
    Collections
    • Chemistry Scholarly Works [553]
    Citation
    Zhu, Z., Hua, D., Clark, D. F., Go, E. P., & Desaire, H. (2013). GlycoPep Detector: A tool for assigning mass spectrometry data of N-linked glycopeptides based on their ETD spectra. Analytical Chemistry, 85(10), 10.1021/ac400287n. http://doi.org/10.1021/ac400287n

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    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

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