A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry
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SciScore for 10.1101/2020.07.27.20161836: (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 institutional ethics committees of National Centre for Disease Control, New Delhi and CSIR-Institute of Genomics and Integrative Biology, Delhi. Sample preparation: Naso and oropharyngeal swab collected in viral transport media (VTM) were inactivated by incubation of samples with lysis buffer (25% guanidinium thiocyanate and 5% SDS) for 20 min at room temperature [12]. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Database search: For viral protein identification, a merged search for 8 DDA runs was … SciScore for 10.1101/2020.07.27.20161836: (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 institutional ethics committees of National Centre for Disease Control, New Delhi and CSIR-Institute of Genomics and Integrative Biology, Delhi. Sample preparation: Naso and oropharyngeal swab collected in viral transport media (VTM) were inactivated by incubation of samples with lysis buffer (25% guanidinium thiocyanate and 5% SDS) for 20 min at room temperature [12]. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Database search: For viral protein identification, a merged search for 8 DDA runs was performed in Protein Pilot software v5.0.1 (Sciex, USA) with paragon algorithm.. Protein Pilotsuggested: NoneResults 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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SciScore for 10.1101/2020.07.27.20161836: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement This study was approved by institutional ethics committees of National Centre for Disease Control, New Delhi and CSIR-Institute of Genomics and Integrative Biology, Delhi. Sample preparation: Naso and oropharyngeal swab collected in viral transport media (VTM) were inactivated by incubation of samples with lysis buffer (25% guanidinium thiocyanate and 5% SDS) for 20 min at room temperature [12]. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Serology test for detection of antibody against SARS-CoV-2 To check if the individuals had developed … SciScore for 10.1101/2020.07.27.20161836: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement This study was approved by institutional ethics committees of National Centre for Disease Control, New Delhi and CSIR-Institute of Genomics and Integrative Biology, Delhi. Sample preparation: Naso and oropharyngeal swab collected in viral transport media (VTM) were inactivated by incubation of samples with lysis buffer (25% guanidinium thiocyanate and 5% SDS) for 20 min at room temperature [12]. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Serology test for detection of antibody against SARS-CoV-2 To check if the individuals had developed antibodies against SARS-CoV-2, we collected blood samples (5 ml) in vacutainer tubes from individuals and separated the plasma by centrifugation. SARS-CoV-2suggested: NoneFor controls, we considered 19 individuals who had negative RT-PCR and did not have any antibodies as evident from negative serology test indicating the absence of IgM and IgG against SARS-CoV-2. IgG against SARS-CoV-2.suggested: NoneSoftware and Algorithms Sentences Resources Database search: For viral protein identification, a merged search for 8 DDA runs was performed in Protein Pilot software v5.0.1 (Sciex, USA) with paragon algorithm.. Protein Pilotsuggested: NoneProtein BLAST search: Protein BLAST search was performed for each of the identified peptide with non-redundant protein sequences (nr) database using NCBI blastp suite by using default parameters for short sequence search. BLASTsuggested: (BLASTX, RRID:SCR_001653)blastpsuggested: (BLASTP, RRID:SCR_001010)JalView tool was used for viewing the consensus of peptides over all the strains [13]. 3. Detection of SARS-CoV-2 specific proteins: 3. i. JalViewsuggested: (Jalview, RRID:SCR_006459)Data availability: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD020574. PRIDEsuggested: (Pride-asap, RRID:SCR_012052)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 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.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
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SciScore for 10.1101/2020.07.27.20161836: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement This study was approved by institutional ethics committees of National Centre for Disease Control, New Delhi and CSIR-Institute of Genomics and Integrative Biology, Delhi. Sample preparation: Naso and oropharyngeal swab collected in viral transport media (VTM) were inactivated by incubation of samples with lysis buffer (25% guanidinium thiocyanate and 5% SDS) for 20 min at room temperature [12]. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Presence of antibodies was detected using Elecsys anti-SARS-CoV-2 on Cobas e411, …SciScore for 10.1101/2020.07.27.20161836: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement This study was approved by institutional ethics committees of National Centre for Disease Control, New Delhi and CSIR-Institute of Genomics and Integrative Biology, Delhi. Sample preparation: Naso and oropharyngeal swab collected in viral transport media (VTM) were inactivated by incubation of samples with lysis buffer (25% guanidinium thiocyanate and 5% SDS) for 20 min at room temperature [12]. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Presence of antibodies was detected using Elecsys anti-SARS-CoV-2 on Cobas e411, anti-SARS-CoV-2suggested: (Abcam Cat# ab272854, RRID:AB_2847844)For controls, we considered 19 individuals who had negative RT-PCR and did not have any antibodies as evident from negative serology test indicating the absence of IgM and IgG against SARS-CoV-2. IgG against SARS-CoV-2.suggested: NoneSoftware and Algorithms Sentences Resources Database search: For viral protein identification, a merged search for 8 DDA runs was performed in Protein Pilot software v5.0.1 (Sciex, USA) with paragon algorithm.. Protein Pilotsuggested: NoneProtein BLAST search: Protein BLAST search was performed for each of the identified peptide with non-redundant protein sequences (nr) database using NCBI blastp suite by using default parameters for short sequence search. blastpsuggested: (BLASTP, RRID:SCR_001010)JalView tool was used for viewing the consensus of peptides over all the strains [13]. 3. Detection of SARS-CoV-2 specific proteins: 3. i. JalViewsuggested: (Jalview, RRID:SCR_006459)Protein BLAST search: We also performed Protein BLAST searches with non-redundant protein sequences (nr) database using NCBI blastp suite. BLASTsuggested: (BLASTX, RRID:SCR_001653)Data availability: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD020574. PRIDEsuggested: (Pride-asap, RRID:SCR_012052)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 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.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
-
SciScore for 10.1101/2020.07.27.20161836: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement This study was approved by institutional ethics committees of National Centre for Disease Control, New Delhi and CSIR-Institute of Genomics and Integrative Biology, Delhi. Sample preparation: Naso and oropharyngeal swab collected in viral transport media (VTM) were inactivated by incubation of samples with lysis buffer (25% guanidinium thiocyanate and 5% SDS) for 20 min at room temperature [12]. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Presence of antibodies was detected using Elecsys anti-SARS-CoV-2 on Cobas e411, …SciScore for 10.1101/2020.07.27.20161836: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement This study was approved by institutional ethics committees of National Centre for Disease Control, New Delhi and CSIR-Institute of Genomics and Integrative Biology, Delhi. Sample preparation: Naso and oropharyngeal swab collected in viral transport media (VTM) were inactivated by incubation of samples with lysis buffer (25% guanidinium thiocyanate and 5% SDS) for 20 min at room temperature [12]. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Presence of antibodies was detected using Elecsys anti-SARS-CoV-2 on Cobas e411, anti-SARS-CoV-2suggested: (Abcam Cat# ab272854, RRID:AB_2847844)For controls, we considered 19 individuals who had negative RT-PCR and did not have any antibodies as evident from negative serology test indicating the absence of IgM and IgG against SARS-CoV-2. IgG against SARS-CoV-2.suggested: NoneSoftware and Algorithms Sentences Resources Database search: For viral protein identification, a merged search for 8 DDA runs was performed in Protein Pilot software v5.0.1 (Sciex, USA) with paragon algorithm.. Protein Pilotsuggested: NoneProtein BLAST search: Protein BLAST search was performed for each of the identified peptide with non-redundant protein sequences (nr) database using NCBI blastp suite by using default parameters for short sequence search. blastpsuggested: (BLASTP, RRID:SCR_001010)JalView tool was used for viewing the consensus of peptides over all the strains [13]. 3. Detection of SARS-CoV-2 specific proteins: 3. i. JalViewsuggested: (Jalview, RRID:SCR_006459)Protein BLAST search: We also performed Protein BLAST searches with non-redundant protein sequences (nr) database using NCBI blastp suite. BLASTsuggested: (BLASTX, RRID:SCR_001653)Data availability: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD020574. PRIDEsuggested: (Pride-asap, RRID:SCR_012052)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 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.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
-
SciScore for 10.1101/2020.07.27.20161836: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement This study was approved by institutional ethics committees of National Centre for Disease Control, New Delhi and CSIR-Institute of Genomics and Integrative Biology, Delhi. Sample preparation: Naso and oropharyngeal swab collected in viral transport media (VTM) were inactivated by incubation of samples with lysis buffer (25% guanidinium thiocyanate and 5% SDS) for 20 min at room temperature [12]. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Serology test for detection of antibody against SARS-CoV-2 To check if the individuals had … SciScore for 10.1101/2020.07.27.20161836: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement This study was approved by institutional ethics committees of National Centre for Disease Control, New Delhi and CSIR-Institute of Genomics and Integrative Biology, Delhi. Sample preparation: Naso and oropharyngeal swab collected in viral transport media (VTM) were inactivated by incubation of samples with lysis buffer (25% guanidinium thiocyanate and 5% SDS) for 20 min at room temperature [12]. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Serology test for detection of antibody against SARS-CoV-2 To check if the individuals had developed antibodies against SARS-CoV-2, we collected blood samples (5 ml) in vacutainer tubes from individuals and separated the plasma by centrifugation. SARS-CoV-2suggested: NoneFor controls, we considered 19 individuals who had negative RT-PCR and did not have any antibodies as evident from negative serology test indicating the absence of IgM and IgG against SARS-CoV-2. IgG against SARS-CoV-2 .suggested: NoneSoftware and Algorithms Sentences Resources Database search: For viral protein identification, a merged search for 8 DDA runs was performed in Protein Pilot software v5.0.1 (Sciex, USA) with paragon algorithm.. Protein Pilotsuggested: NoneProtein BLAST search: Protein BLAST search was performed for each of the identified peptide with non-redundant protein sequences (nr) database using NCBI blastp suite by using default parameters for short sequence search. blastpsuggested: (BLASTP, SCR_001010)JalView tool was used for viewing the consensus of peptides over all the strains [13]. 3. Detection of SARS-CoV-2 specific proteins: 3. i. JalViewsuggested: (Jalview, SCR_006459)Protein BLAST search: We also performed Protein BLAST searches with non-redundant protein sequences (nr) database using NCBI blastp suite. BLASTsuggested: (BLASTX, SCR_001653)Data availability: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD020574. PRIDEsuggested: (Pride-asap, SCR_012052)Data from additional tools added to each annotation on a weekly basis.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
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