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    GlycoPep MassList: Software to Generate Massive Inclusion Lists for Glycopeptide Analyses

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    Issue Date
    2017-01
    Author
    Hu, Wenting
    Su, Xiaomeng
    Zhu, Zhikai
    Go, Eden P.
    Desaire, Heather
    Publisher
    Springer Verlag
    Type
    Article
    Article Version
    Scholarly/refereed, author accepted manuscript
    Rights
    The final publication is available at Springer via http://dx.doi.org/10.1007/s00216-016-9896-y
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    Abstract
    Protein glycosylation drives many biological processes and serves as markers for disease; therefore, the development of tools to study glycosylation is an essential and growing area of research. Mass spectrometry can be used to identify both the glycans of interest and the glycosylation sites to which those glycans are attached, when proteins are proteolytically digested and their glycopeptides are analyzed by a combination of high-resolution mass spectrometry (MS) and tandem mass spectrometry (MS/MS) methods. One major challenge in these experiments is collecting the requisite MS/MS data. The digested glycopeptides are often present in complex mixtures and in low abundance, and the most commonly used approach to collect MS/MS data on these species is data-dependent acquisition (DDA), where only the most intense precursor ions trigger MS/MS. DDA results in limited glycopeptide coverage. Semi-targeted data acquisition is an alternative experimental approach that can alleviate this difficulty. However, due to the massive heterogeneity of glycopeptides, it is not obvious how to expediently generate inclusion lists for these types of analyses. To solve this problem, we developed the software tool GlycoPep MassList, which can be used to generate inclusion lists for liquid chromatography tandem-mass spectrometry (LC-MS/MS) experiments. The utility of the software was tested by conducting comparisons between semi-targeted and untargeted data-dependent analysis experiments on a variety of proteins, including IgG, a protein whose glycosylation must be characterized during its production as a biotherapeutic. When the GlycoPep MassList software was used to generate inclusion lists for LC-MS/MS experiments, more unique glycopeptides were selected for fragmentation. Generally, ∼30 % more unique glycopeptides can be analyzed per protein, in the simplest cases, with low background. In cases where background ions from proteins or other interferents are high, usage of an inclusion list is even more advantageous. The software is freely publically accessible.
    URI
    http://hdl.handle.net/1808/24877
    DOI
    https://doi.org/10.1007/s00216-016-9896-y
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    • Chemistry Scholarly Works [506]
    Citation
    Hu, W., Su, X., Zhu, Z., Go, E. P., & Desaire, H. (2017). GlycoPep MassList: Software to Generate Massive Inclusion Lists for Glycopeptide Analyses. Analytical and Bioanalytical Chemistry, 409(2), 561–570. http://doi.org/10.1007/s00216-016-9896-y

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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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