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A review of methods for interpretation of glycopeptide tandem mass spectral data

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Abstract

Despite the publication of several software tools for analysis of glycopeptide tandem mass spectra, there remains a lack of consensus regarding the most effective and appropriate methods. In part, this reflects problems with applying standard methods for proteomics database searching and false discovery rate calculation. While the analysis of small post-translational modifications (PTMs) may be regarded as an extension of proteomics database searching, glycosylation requires specialized approaches. This is because glycans are large and heterogeneous by nature, causing glycopeptides to exist as multiple glycosylated variants. Thus, the mass of the peptide cannot be calculated directly from that of the intact glycopeptide. In addition, the chemical nature of the glycan strongly influences product ion patterns observed for glycopeptides. As a result, glycopeptidomics requires specialized bioinformatics methods. We summarize the recent progress towards a consensus for effective glycopeptide tandem mass spectrometric analysis.

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Acknowledgments

The authors are supported by NIH grant P41GM104603. Thermo-Fisher Scientific provided instrument time for the acquisition of tandem mass spectra shown in Fig. 1.

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Authors and Affiliations

  1. Department of Biochemistry, Boston University, Medical Campus, 670 Albany St., Rm. 509, Boston, MA, 02118, USA

    Kshitij Khatri, Nancy Leymarie & Joseph Zaia

  2. Center for Biomedical Mass Spectrometry, Boston University, Boston, MA, USA

    Han Hu, Kshitij Khatri, Joshua Klein, Nancy Leymarie & Joseph Zaia

  3. Bioinformatics Program, Boston University, Boston, MA, USA

    Han Hu, Joshua Klein & Joseph Zaia

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  1. Han Hu
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  2. Kshitij Khatri
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Correspondence to Joseph Zaia.

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Hu, H., Khatri, K., Klein, J. et al. A review of methods for interpretation of glycopeptide tandem mass spectral data. Glycoconj J 33, 285–296 (2016). https://doi.org/10.1007/s10719-015-9633-3

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  • DOI: https://doi.org/10.1007/s10719-015-9633-3

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