Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window

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1. Version published to 10.1021/acs.jproteome.0c00535

   Jul 22, 2020
2. 

   ScreenIT

   Jun 21, 2020

   SciScore for 10.1101/2020.06.19.161000: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: This study was approved by the institutional review boards of the University Hospital of Nîmes, France (2020-05-01).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Infection and virus purification: Vero E6 cells (1×106) seeded into 150 cm2 flasks were grown to cell confluence in 15 ml DMEM supplemented with 5% FCS and 0.5% penicillin–streptomycin for one night at 37°C under 9% CO2.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   MS/MS spectra from the simili SARS-CoV-2 …

   SciScore for 10.1101/2020.06.19.161000: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: This study was approved by the institutional review boards of the University Hospital of Nîmes, France (2020-05-01).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Infection and virus purification: Vero E6 cells (1×106) seeded into 150 cm2 flasks were grown to cell confluence in 15 ml DMEM supplemented with 5% FCS and 0.5% penicillin–streptomycin for one night at 37°C under 9% CO2.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   MS/MS spectra from the simili SARS-CoV-2 contaminated swabs and from the COVID-19 nasopharyngeal swabs were assigned with the MASCOT Daemon 2.3.2 search engine	MASCOT Daemon suggested: None
   MS1 peak areas were evaluated with Skyline (27).	Skyline suggested: (Skyline, RRID:SCR_014080)
   Briefly, we created spectral libraries based on the DAT files from each MASCOT search (cut-of 0.99) and uploaded the MS1 full scan information contained in the raw files.	MASCOT suggested: (Mascot, RRID:SCR_014322)
   Mass spectrometry and proteomics data: The mass spectrometry and proteomics data acquired on simili swabs have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (28) with the dataset identifiers PXD019686 and 10.6019/PXD019686.	PRIDE suggested: (Pride-asap, RRID:SCR_012052)

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   Results from OddPub: Thank you for sharing your data.

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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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   Read the original source
3. 

   Version published to 10.1101/2020.06.19.161000v1 on bioRxiv

   Jun 19, 2020