Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection
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SciScore for 10.1101/2020.04.27.20081810: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: All patients with SARS-CoV-2 infection proven by positive PCR from respiratory specimens and willing to provide written informed consent are eligible for inclusion.
IRB: The Pa-COVID-19 study is carried out according to the Declaration of Helsinki and the principles of Good Clinical Practice (ICH 1996) where applicable and was approved by the ethics committee of Charité- Universitätsmedizin Berlin (EA2/066/20)Randomization Generation Scotland study: 199 serum samples from random individuals that participated in the Generation Scotland (GS) epidemiological study (Smith et al., 2013) were used. Blinding not detected. Power Analysis not detected. Sex as a … SciScore for 10.1101/2020.04.27.20081810: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: All patients with SARS-CoV-2 infection proven by positive PCR from respiratory specimens and willing to provide written informed consent are eligible for inclusion.
IRB: The Pa-COVID-19 study is carried out according to the Declaration of Helsinki and the principles of Good Clinical Practice (ICH 1996) where applicable and was approved by the ethics committee of Charité- Universitätsmedizin Berlin (EA2/066/20)Randomization Generation Scotland study: 199 serum samples from random individuals that participated in the Generation Scotland (GS) epidemiological study (Smith et al., 2013) were used. 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 ) and K562 cell lysate (MS Compatible Human Protein Extract, Digest, V6951) were purchased from Promega. K562suggested: NoneSoftware and Algorithms Sentences Resources Data availability: The raw data of the acquired commercial plasma and serum control samples within the GS study was submitted to the ProteomeXchange Consortium via PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset submission #413758. PRIDEsuggested: (Pride-asap, RRID:SCR_012052)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:To account for this biological limitation, we applied very strict filtering to the dataset, namely, we only tested for differential abundance of proteins which had at least five different peptide precursors identified at least in one of the acquisitions. We identified 37 protein groups with either increasing or decreasing levels, depending on the severity of the disease (0.05 significance, multiple testing-corrected, Theil-Sen test against the WHO severity score; see Methods for testing methodology) (Figure 4c and Table S3). Next, to validate the biomarkers, we processed the validation cohort (Table S1), and recorded 96 proteomes in triplicates for 15 healthy volunteers, and 17 COVID-19 patients (Table S1). The experiment quantified 319 protein groups among which 248 unique proteins were detected with 85% data completeness. Despite being conducted on a different matrix (citrate plasma), this independent study confirmed 27 of the protein groups with either increasing or decreasing levels (A1BG, ACTB;ACTG1, ALB, APOA1, APOC1, C1R, C1S, C8A, CD14, CFB, CFH, CFI, CRP, FGA, FGB, FGG, GSN, HP, ITIH3, ITIH4, LBP, LGALS3BP, LRG1, SAA1, SAA1;SAA2, SERPINA10, TF; 0.05 significance, multiple testing-corrected). This set of proteins thus represents potential biomarkers of disease severity. Out of the remaining 10 proteins, 9 (AGT, AZGP1, C2, C7, C8B, CLU, CPN1, PLG, VTN) did not reach statistical significance in the smaller validation group, while the IGHG2;IGHG3 protein group showed the...
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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