Identification, mapping and relative quantitation of SARS-CoV-2 Spike glycopeptides by Mass-Retention Time Fingerprinting

  1. Rod Chalk
  2. William E. P. Greenland
  3. Tiago Moreira
  4. Jesse Coker
  5. Shubhashish M. M. Mukhopadhyay
  6. Eleanor Williams
  7. Charlotte Manning
  8. Tina Bohstedt
  9. Rama McCrorie
  10. Alejandra Fernandez-Cid
  11. Nicola A. Burgess-Brown

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Abstract

We describe an analytical method for the identification, mapping and relative quantitation of glycopeptides from SARS-CoV-2 Spike protein. The method may be executed using a LC-TOF mass spectrometer, requires no specialized knowledge of glycan analysis and exploits the differential resolving power of reverse phase HPLC. While this separation technique resolves peptides with high efficiency, glycans are resolved poorly, if at all. Consequently, glycopeptides consisting of the same peptide bearing different glycan structures will all possess very similar retention times and co-elute. Rather than a disadvantage, we show that shared retention time can be used to map multiple glycan species to the same peptide and location. In combination with MSMS and pseudo MS3, we have constructed a detailed mass-retention time database for Spike glycopeptides. This database allows any accurate mass LC-MS laboratory to reliably identify and quantify Spike glycopeptides from a single overnight elastase digest in less than 90 minutes.

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  1. Version published to 10.1038/s42003-021-02455-w
  2. Version published to 10.1101/2020.07.24.217562v2 on bioRxiv
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    Table 2: Resources

    Software and Algorithms
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    This is possible either using the Agilent software described, software provided by other vendors, or by manual inspection.
    Agilent
    suggested: (Agilent Bravo NGS, RRID:SCR_019473)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

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  4. Version published to 10.1101/2020.07.24.217562v1 on bioRxiv