Procedural Rigor and Reproducibility in NMR Metabolomics: Community Practices and Challenges

Nuclear magnetic resonance (NMR) spectroscopy is a fundamental tool of metabolomics, valued for its reproducibility, quantitative accuracy and broad applicability across biological, chemical and clinical sciences. However, methodological inconsistencies, insufficient protocol reporting and limited infrastructure continue to hinder reproducibility and data sharing. To assess the current state of NMR metabolomics practice, we developed a comprehensive questionnaire and distributed it worldwide to researchers engaged in NMR-based metabolomics. We received 75 responses from a diverse cohort of investigators from academia, clinics and core facilities. The survey focused on Quality Assurance (QA) and Quality Control (QC) practices and provides an overview of the current status of NMR metabolomics and its implementation. Results reveal that while 86% of laboratories have Standard Operating Procedures (SOPs), deviations from these protocols are common and often undocumented, undermining reproducibility. QC practices, including pooled samples and system suitability checks, are widely recognized, but their implementation is inconsistent. Data accessibility remains limited, with fewer than 10% of respondents routinely depositing raw or processed spectral data in public repositories. Formal regulatory oversight and dedicated QA personnel are uncommon. Training is largely informal, with substantial gaps in areas such as data analysis and statistics, raising concerns about knowledge transfer and methodological consistency. Our findings describe a technically skilled community that is constrained by variations in NMR infrastructure and inconsistent implementation of best practices. Addressing these issues through adaptive standardization, structured training programs, and stronger institutional support is critical for advancing transparency, reproducibility and impact of NMR in metabolomics.