Introduction

Mass spectrometry has become a routine experimental tool for proteomic biomarker analysis of human blood samples, partly due to the large availability of informatics tools. As one of the most common protein post-translational modifications (PTMs) in mammals, protein glycosylation has been observed to alter in multiple human diseases and thus may potentially be candidate markers of disease progression. While mass spectrometry instrumentation has seen advancements in capabilities, discovering glycosylation-related markers using existing software is currently not straightforward. Complete characterization of protein glycosylation requires the identification of intact glycopeptides in samples, including identification of the modification site as well as the structure of the attached glycans. In this paper, we present GlycoSeq, an open-source software tool that implements a heuristic iterated glycan sequencing algorithm coupled with prior knowledge for automated elucidation of the glycan structure within a glycopeptide from its collision-induced dissociation tandem mass spectrum. GlycoSeq employs rules of glycosidic linkage as defined by glycan synthetic pathways to eliminate improbable glycan structures and build reasonable glycan trees. We tested the tool on two sets of tandem mass spectra of N-linked glycopeptides cell lines acquired from breast cancer patients. After employing enzymatic specificity within the N-linked glycan synthetic pathway, the sequencing results of GlycoSeq were highly consistent with the manually curated glycan structures. Hence, GlycoSeq is ready to be used for the characterization of glycan structures in glycopeptides from MS/MS analysis. GlycoSeq is released as open source software at https://github.com/chpaul/GlycoSeq/ .

Publications

  1. Automated Glycan Sequencing from Tandem Mass Spectra of N-Linked Glycopeptides.
    Cite this
    Yu CY, Mayampurath A, Zhu R, Zacharias L, Song E, Wang L, Mechref Y, Tang H, 2016-06-01 - Analytical Chemistry

Credits

  1. Chuan-Yih Yu
    Developer

    School of Informatics and Computing, Indiana University, United States of America

  2. Anoop Mayampurath
    Developer

    Computation Institute, University of Chicago, United States of America

  3. Rui Zhu
    Developer

    Department of Chemistry and Biochemistry, Texas Tech University, United States of America

  4. Lauren Zacharias
    Developer

    Department of Chemistry and Biochemistry, Texas Tech University, United States of America

  5. Ehwang Song
    Developer

    Department of Chemistry and Biochemistry, Texas Tech University, United States of America

  6. Lei Wang
    Developer

    School of Informatics and Computing, Indiana University, United States of America

  7. Yehia Mechref
    Developer

    Department of Chemistry and Biochemistry, Texas Tech University, United States of America

  8. Haixu Tang
    Investigator

    School of Informatics and Computing, Indiana University, United States of America

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Summary
AccessionBT000678
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByHaixu Tang