Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire

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1. Version published to 10.1021/acs.jproteome.1c00882

   Dec 8, 2021
2. 

   ScreenIT

   Jul 10, 2021

   SciScore for 10.1101/2021.07.06.21259226: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Plasma from a convalescent patient featuring a high titer of anti-SARS-CoV-2-RBD antibodies was purchased from AllCells (commercial sample 1 – CS1) and used as a standard positive control throughout the study.	anti-SARS-CoV-2-RBD suggested: None
   Human recombinant monoclonal Anti-SARS-CoV-2 antibody, mAb CR3022 produced in Nicotiana bethamiana (tobacco plant) was obtained from Novici Biotech LLC (Lot NCV_051520B) as a 1.0 mg/mL solution in PBS (pH 7.2).	Anti-SARS-CoV-2 suggested: (Abcam Cat# ab273074, RRID:AB_2847846)
   Western …

   SciScore for 10.1101/2021.07.06.21259226: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Plasma from a convalescent patient featuring a high titer of anti-SARS-CoV-2-RBD antibodies was purchased from AllCells (commercial sample 1 – CS1) and used as a standard positive control throughout the study.	anti-SARS-CoV-2-RBD suggested: None
   Human recombinant monoclonal Anti-SARS-CoV-2 antibody, mAb CR3022 produced in Nicotiana bethamiana (tobacco plant) was obtained from Novici Biotech LLC (Lot NCV_051520B) as a 1.0 mg/mL solution in PBS (pH 7.2).	Anti-SARS-CoV-2 suggested: (Abcam Cat# ab273074, RRID:AB_2847846)
   Western blot identification of enriched antibody isotypes: An enrichment was performed as described in the section “Enrichment of RBD-reactive antibodies from patient samples” above to screen for the presence of individual human antibody isotypes (IgG1, IgG2, IgG3, IgG4, IgA, IgD, IgE, and IgM).	IgM suggested: None
   Anti-RBD antibody quantification: Titers of antibodies from patient plasma responsive to SARS-CoV-2 RBD were measured using Lumit™ Dx SARS-CoV-2 Immunoassay (Promega VB1080).	Anti-RBD suggested: None
   Recombinant DNA
   Sentences	Resources
   Recombinant expression of SARS-CoV-2 spike protein receptor-binding (RBD) domain: The plasmid pCAGGS SARS-CoV-2 RBD comprises an N-terminal signal sequence, amino acids 319-541 of the spike protein from SARS-CoV-2 (the receptor-binding domain, RBD), and a C-terminal 6-His tag34.	pCAGGS SARS-CoV-2 suggested: None
   Vector pCAGGS Containing the SARS-Related Coronavirus 2, Wuhan-Hu-1	pCAGGS suggested: RRID:Addgene_18926)
   Software and Algorithms
   Sentences	Resources
   Proteins were identified from the tandem mass spectra extracted by Xcalibur version 4.0.	Xcalibur suggested: (Thermo Xcalibur, RRID:SCR_014593)
   MS2 spectra were searched against the Spike protein RBD and SwissProt Homo sapiens database using Mascot search engine (Matrix Science, London, UK; version 2.7.0).	Mascot suggested: (Mascot, RRID:SCR_014322)
   A total of 70 μL of the sample was sprayed through an Ion Max Source (Thermo Fisher Scientific) fitted with a HESI II probe at a flow rate of 1 μL/min delivered by a PAL3 robot (CTC Analytics) and analyzed by a Q Exactive Plus mass spectrometer (Thermo Fisher Scientific)37, 38.	Thermo Fisher Scientific)37 suggested: None
   MS data were processed using Skyline (Version 20.2).	Skyline suggested: (Skyline, RRID:SCR_014080)
   Statistical analysis: ANOVA statistics were calculated using SAS (SAS Institute, Cary, NC).	SAS Institute suggested: (Statistical Analysis System, RRID:SCR_008567)
   Person’s correlations were calculated using the function “cor.test” and method “pearson” on RStudio v3.1.1073.	RStudio suggested: (RStudio, RRID:SCR_000432)
   Violin and dot plots were generated with GraphPad Prism 9.0.2 and that same software was used for calculating the statistical significance by one-way ANOVA with Tukey’s multiple comparison test (* p<0.05; ** p<0.01).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Data and software availability: Processed datasets utilized for the IgMS analyses can be found on the MassiVE repository, MSV000087529, after puplication.	MassiVE suggested: None

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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.
   • Thank you for including a protocol registration statement.

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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2021.07.06.21259226v1 on medRxiv

   Jul 7, 2021