A Tool to Encourage Minimum Reporting Guideline Uptake for Data Analysis in Metabolomics

Considine, Elizabeth C.; Salek, Reza M.

doi:10.3390/metabo9030043

Cited by 25 publications

(26 citation statements)

References 40 publications

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“…Spectral quality control via metabolomics standard initiative identified two samples that failed due to salt precipitation and as such were removed from further analyses. 54 , 61 Following metabolite identification and quantification, one sample was identified as an outlier and subsequently removed from statistical analyses. Isopropanol was identified within all media samples.…”

Section: Resultsmentioning

confidence: 99%

Ex Vivo Equine Cartilage Explant Osteoarthritis Model: A Metabolomics and Proteomics Study

et al. 2020

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Osteoarthritis is an age-related degenerative musculoskeletal disease characterized by loss of articular cartilage, synovitis, and subchondral bone sclerosis. Osteoarthritis pathogenesis is yet to be fully elucidated with no osteoarthritis-specific biomarkers in clinical use. Ex vivo equine cartilage explants ( n = 5) were incubated in tumor necrosis factor-α (TNF-α)/interleukin-1β (IL-1β)-supplemented culture media for 8 days, with the media removed and replaced at 2, 5, and 8 days. Acetonitrile metabolite extractions of 8 day cartilage explants and media samples at all time points underwent one-dimensional (1D) 1 H nuclear magnetic resonance metabolomic analysis, with media samples also undergoing mass spectrometry proteomic analysis. Within the cartilage, glucose and lysine were elevated following TNF-α/IL-1β treatment, while adenosine, alanine, betaine, creatine, myo-inositol, and uridine decreased. Within the culture media, 4, 4, and 6 differentially abundant metabolites and 154, 138, and 72 differentially abundant proteins were identified at 1–2, 3–5, and 6–8 days, respectively, including reduced alanine and increased isoleucine, enolase 1, vimentin, and lamin A/C following treatment. Nine potential novel osteoarthritis neopeptides were elevated in the treated media. Implicated pathways were dominated by those involved in cellular movement. Our innovative study has provided insightful information on early osteoarthritis pathogenesis, enabling potential translation for clinical markers and possible new therapeutic targets.

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Section: Resultsmentioning

confidence: 99%

Ex Vivo Equine Cartilage Explant Osteoarthritis Model: A Metabolomics and Proteomics Study

et al. 2020

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“…Penelope is currently being integrated and tested in an online journal submission application 14–16. A recent study also developed a writing tool, and a template with the minimum amount of information to report regarding data handling of biomarkers in metabolomics 17. Nevertheless, none of these efforts focuses on the uptake of several reporting guidelines during the writing process, using common offline writing platforms such as Microsoft Word.…”

Section: Introductionmentioning

confidence: 99%

Usefulness of applying research reporting guidelines as Writing Aid software: a crossover randomised controlled trial

et al. 2019

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ObjectivesTo assess the intention of using a Writing Aid software, which integrates four research reporting guidelines (Consolidated Standards of Reporting Trials, Preferred Reporting Items for Systematic Reviews and Meta-Analyses, Strengthening the Reporting of Observational Studies in Epidemiology and STrengthening the Reporting of Observational Studies in Epidemiology-nutritional epidemiology) and their Elaboration & Explanation (E&E) documents during the write-up of research in Microsoft Word compared with current practices.DesignTwo-arms crossover randomised controlled trial with no blinding and no washout period.SettingFace-to-face or online sessions.Participants54 (28 in arm 1 and 26 in arm 2) doctoral and postdoctoral researchers.InterventionsReporting guidelines and their E&E document were randomly administered as Writing Aid or as Word documents in a single 30 min to 1 hour session, with a short break before crossing over to the other study intervention.Primary and secondary outcomesUsing the Technology Acceptance Model, we assessed the primary outcome: the difference in the mean of intention of use; and secondary outcomes: the difference in mean perceived ease of use and perceived usefulness. The three outcomes were measured using questions with a 7-point Likert-scale. Secondary analysis using structural equation modelling (SEM) was applied to explore the relationships between the outcomes.ResultsNo significant difference in reported intention of use (mean difference and 95% CI 0.25 (–0.05 to 0.55), p=0.10), and perceived usefulness (mean difference and 95% CI 0.19 (–0.04 to 0.41), p=0.10). The Writing Aid performed significantly better than the word document on researchers’ perceived ease of use (mean difference and 95% CI 0.59 (0.29 to 0.89), p<0.001). In the SEM analysis, participants’ intention of using the tools was indirectly affected by perceived ease of use (beta 0.53 p=0.002).ConclusionsDespite no significant difference in the intention of use between the tools, administering reporting guidelines as Writing Aid is perceived as easier to use, offering a possibility to further explore its applicability to enhance reporting adherence.

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“…The QUADOMICs tool, an adaptation for omics study of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS), assesses the methodological quality of omics-based diagnostic studies, and could be considered as a prototype to help develop an appropriate guideline for metabolomics [149]. Recently, a novel reporting guideline based on R Markdown template for the data analysis step of biomarker discovery metabolomics studies has been issued [150]. The new guideline, along with our suggested one in reference to STROBE, TRIPOD, and QUADOMICs, if applied, will improve the completeness, transparency, and reproducibility of clinical lipidomics and metabolomics study (Table 3).…”

Section: Fundamental Requirements On Standards For Reporting Metabolomentioning

confidence: 99%

Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine

et al. 2020

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Despite the tremendous success, pitfalls have been observed in every step of a clinical metabolomics workflow, which impedes the internal validity of the study. Furthermore, the demand for logistics, instrumentations, and computational resources for metabolic phenotyping studies has far exceeded our expectations. In this conceptual review, we will cover inclusive barriers of a metabolomics-based clinical study and suggest potential solutions in the hope of enhancing study robustness, usability, and transferability. The importance of quality assurance and quality control procedures is discussed, followed by a practical rule containing five phases, including two additional “pre-pre-” and “post-post-” analytical steps. Besides, we will elucidate the potential involvement of machine learning and demonstrate that the need for automated data mining algorithms to improve the quality of future research is undeniable. Consequently, we propose a comprehensive metabolomics framework, along with an appropriate checklist refined from current guidelines and our previously published assessment, in the attempt to accurately translate achievements in metabolomics into clinical and epidemiological research. Furthermore, the integration of multifaceted multi-omics approaches with metabolomics as the pillar member is in urgent need. When combining with other social or nutritional factors, we can gather complete omics profiles for a particular disease. Our discussion reflects the current obstacles and potential solutions toward the progressing trend of utilizing metabolomics in clinical research to create the next-generation healthcare system.

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A Tool to Encourage Minimum Reporting Guideline Uptake for Data Analysis in Metabolomics

Cited by 25 publications

References 40 publications

Ex Vivo Equine Cartilage Explant Osteoarthritis Model: A Metabolomics and Proteomics Study

Ex Vivo Equine Cartilage Explant Osteoarthritis Model: A Metabolomics and Proteomics Study

Usefulness of applying research reporting guidelines as Writing Aid software: a crossover randomised controlled trial

Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine

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