Volume 8 Issue 5-6
Dec.  2022
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Jiechen Shen, Zexuan Chen, Shisheng Sun. Identifying intact N-glycopeptides from tandem mass spectrometry data using StrucGP[J]. Biophysics Reports, 2022, 8(5-6): 282-300. doi: 10.52601/bpr.2022.220010
Citation: Jiechen Shen, Zexuan Chen, Shisheng Sun. Identifying intact N-glycopeptides from tandem mass spectrometry data using StrucGP[J]. Biophysics Reports, 2022, 8(5-6): 282-300. doi: 10.52601/bpr.2022.220010

Identifying intact N-glycopeptides from tandem mass spectrometry data using StrucGP

doi: 10.52601/bpr.2022.220010
Funds:  This work was supported by the National Key Research and Development Program of China (2019YFA09005200), and the National Natural Science Foundation of China (91853123, 81773180). The authors would like to thank Dr. Mengqiu Dong and Dr. Yong Cao from the National Institute of Biological Sciences (Beijing) for their evaluation and kind suggestions on this protocol.
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  • Corresponding author: suns@nwu.edu.cn (S. Sun)
  • Received Date: 23 May 2022
  • Accepted Date: 03 August 2022
  • Available Online: 04 April 2023
  • Publish Date: 31 December 2022
  • Protein glycosylation is of great importance in many biological processes. Glycosylation has been increasingly analyzed at the intact glycopeptide level using mass spectrometry to study site-specific glycosylation changes under different physiological and pathological conditions. StrucGP is a glycan database-independent search engine for the structural interpretation of N-glycoproteins at the site-specific level. To ensure the accuracy of results, two collision energies are implemented in instrument settings for each precursor to separate fragments of peptides and glycans. In addition, the false discovery rates (FDR) of peptides and glycans as well as probabilities of detailed structures are estimated. In this protocol, the use of StrucGP is demonstrated, including environment configuration, data preprocessing as well as result inspection and visualization using our in-house software “GlycoVisualTool”. The described workflow should be able to be performed by anyone with basic proteomic knowledge.

  • Jiechen Shen, Zexuan Chen, and Shisheng Sun declare that they have no conflict of interest.
    This article does not contain any studies with human or animal subjects performed by any of the authors.

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