MALDI-TOF mass spectrometry of saliva samples as a prognostic tool for COVID-19

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1. Version published to 10.1080/20002297.2022.2043651

   Feb 27, 2022
2. 

   ScreenIT

   Dec 17, 2021

   SciScore for 10.1101/2021.12.10.21267596: (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

   Software and Algorithms
   Sentences	Resources
   First, fid files were converted to mzML using MSconvert available in ProteoWizard (version: 3.0.20220) 26.	ProteoWizard suggested: (ProteoWizard, RRID:SCR_012056)
   The spectra for each sample were transformed (square root), smoothed (Savitzky-Golay and halfWindowSize of 10) 28 and the base line corrected using the TopHat algorithm 29.	TopHat suggested: (TopHat, RRID:SCR_013035)

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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: We detected the …

   SciScore for 10.1101/2021.12.10.21267596: (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

   Software and Algorithms
   Sentences	Resources
   First, fid files were converted to mzML using MSconvert available in ProteoWizard (version: 3.0.20220) 26.	ProteoWizard suggested: (ProteoWizard, RRID:SCR_012056)
   The spectra for each sample were transformed (square root), smoothed (Savitzky-Golay and halfWindowSize of 10) 28 and the base line corrected using the TopHat algorithm 29.	TopHat suggested: (TopHat, RRID:SCR_013035)

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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: We detected the following sentences addressing limitations in the study:

   However, it is important to note the limitations of this technique. We observed high inter-sample variation, which can reduce the performance of the models trained and reduce even more the performance during model generalization (validation with unseen data). This could be minimized by adding more samples to the cohort or by using more elaborate sample preparation methods. Therefore, a larger cohort should be analyzed to develop more robust models and inter-laboratory samples should be used to validate the findings. Moreover, improvements in the analytical part should be able to discriminate better between MILD and MODERATE groups.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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

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   Read the original source
3. 

   Version published to 10.1101/2021.12.10.21267596 on medRxiv

   Dec 14, 2021