Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications

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1. Version published to 10.1016/j.eng.2020.07.014

   Oct 1, 2021
2. 

   ScreenIT

   Jun 6, 2020

   SciScore for 10.1101/2020.04.29.068098: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Expression and purification of HCoV-19 spike ectodomain and hACE2: HCoV-19 S gene (virus isolate: Wuhan Hu-1; GenBank number QHD43416.1) was synthesized (Genscript) with codons optimized for insect cell expression.	HCoV-19 suggested: None
   The extracellular domain of hACE2 (Gln18-Ser740, NP_068576.1) with C-terminal Fc tag was expressed in HEK 293 cells were purified by protein A sepharose beads (GE Healthcare).	HEK 293 suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)
   Software and Algorithms
   Sentences	Resources
   The MS and MS/MS spectra were recorded using the Xcalibur software 2.3 …

   SciScore for 10.1101/2020.04.29.068098: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Expression and purification of HCoV-19 spike ectodomain and hACE2: HCoV-19 S gene (virus isolate: Wuhan Hu-1; GenBank number QHD43416.1) was synthesized (Genscript) with codons optimized for insect cell expression.	HCoV-19 suggested: None
   The extracellular domain of hACE2 (Gln18-Ser740, NP_068576.1) with C-terminal Fc tag was expressed in HEK 293 cells were purified by protein A sepharose beads (GE Healthcare).	HEK 293 suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)
   Software and Algorithms
   Sentences	Resources
   The MS and MS/MS spectra were recorded using the Xcalibur software 2.3 (Thermo Scientific, USA)	Xcalibur suggested: (Thermo Xcalibur, RRID:SCR_014593)
   Bioinformatics: The acquired MS raw files from deglycosylated peptides were searched by MaxQuant (version 1.6.10.43) against the human ACE2 sequence from UniProtKB and HCoV-19 S sequence (YP_009724390.1_3) from NCBI.	MaxQuant suggested: (MaxQuant, RRID:SCR_014485) UniProtKB suggested: (UniProtKB, RRID:SCR_004426)
   The modified residues within each model were generated with Coot (Emsley et al., 2010).	Coot suggested: (Coot, RRID:SCR_014222)
   All structural figures were performed by PyMOL (Schrödinger Inc. U.S.A.).	PyMOL suggested: (PyMOL, RRID:SCR_000305)

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   Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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

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

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   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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3. 

   Version published to 10.1101/2020.04.29.068098v1 on bioRxiv

   Apr 29, 2020