Current Practices in LC-MS Untargeted Metabolomics: A Scoping Review on the Use of Pooled Quality Control Samples

• Autores: Broeckling, Corey D.; Beger, Richard D.; Cheng, Leo L.; Cumeras, Raquel; Cuthbertson, Daniel J.; Dasari, Surendra; Davis, W. Clay; Dunn, Warwick B.; Evans, Anne Marie; Fernández Ochoa, Alvaro; Gika, Helen; Goodacre, Royston; Goodman, Kelli D.; Gouveia, Goncalo J.; Hsu, Ping-Ching; Kirwan, Jennifer A.; Kodra, Dritan; Kuligowski, Julia; Lan, Renny Shang-Lun; Monge, Maria Eugenia; Moussa, Laura W.; Nair, Sindhu G.; Reisdorph, Nichole; Sherrod, Stacy D.; Ulmer Holland, Candice; Vuckovic, Dajana; Yu, Li-Rong; Zhang, Bo; Theodoridis, Georgios; Mosley, Jonathan D.
• Año de publicación: 2023
• Idioma: inglés
• Tipo de recurso: artículo
• Materia: METABOLOMICS; LC-MS; QUALITY CONTROL; QUALITY ASSURANCE
• Institución: Consejo Nacional de Investigaciones Científicas y Técnicas

Untargeted metabolomics is an analytical approach with numerous applications serving as an effective metabolic phenotyping platform to characterize small molecules within a biological system. Data quality can be challenging to evaluate and demonstrate in metabolomics experiments. This has driven the use of pooled quality control (QC) samples for monitoring and, if necessary, correcting for analytical variance introduced during sample preparation and data acquisition stages. Described herein is a scoping literature review detailing the use of pooled QC samples in published untargeted liquid chromatography-mass spectrometry (LC-MS) based metabolomics studies. A literature query was performed, the list of papers was filtered, and suitable articles were randomly sampled. In total, 109 papers were each reviewed by at least five reviewers, answering predefined questions surrounding the use of pooled quality control samples. The results of the review indicate that use of pooled QC samples has been relatively widely adopted by the metabolomics community and that it is used at a similar frequency across biological taxa and sample types in both small- and large-scale studies. However, while many studies generated and analyzed pooled QC samples, relatively few reported the use of pooled QC samples to improve data quality. This demonstrates a clear opportunity for the field to more frequently utilize pooled QC samples for quality reporting, feature filtering, analytical drift correction, and metabolite annotation. Additionally, our survey approach enabled us to assess the ambiguity in the reporting of the methods used to describe the generation and use of pooled QC samples. This analysis indicates that many details of the QC framework are missing or unclear, limiting the reader’s ability to determine which QC steps have been taken. Collectively, these results capture the current state of pooled QC sample usage and highlight existing strengths and deficiencies as they are applied in untargeted LC-MS metabolomics.
Fil: Broeckling, Corey D.. State University of Colorado - Fort Collins; Estados Unidos
Fil: Beger, Richard D.. Us Food And Drug Administracion; Estados Unidos
Fil: Cheng, Leo L.. Harvard Medical School; Estados Unidos
Fil: Cumeras, Raquel. Universitat Rovira I Virgili; España
Fil: Cuthbertson, Daniel J.. Agilent Technologies; Estados Unidos
Fil: Dasari, Surendra. Mayo Clinic Cancer Center; Estados Unidos
Fil: Davis, W. Clay. United States Departament Of Commerce. National Institute Of Standars And Technology; Estados Unidos
Fil: Dunn, Warwick B.. University of Liverpool; Reino Unido
Fil: Evans, Anne Marie. Metabolon; Estados Unidos
Fil: Fernández Ochoa, Alvaro. Universidad de Granada; España
Fil: Gika, Helen. Aristotle University Of Thessaloniki; Grecia
Fil: Goodacre, Royston. University of Liverpool; Reino Unido
Fil: Goodman, Kelli D.. Metabolon, Inc.; Estados Unidos
Fil: Gouveia, Goncalo J.. University of Maryland; Estados Unidos
Fil: Hsu, Ping-Ching. University of Arkansas for Medical Sciences; Estados Unidos
Fil: Kirwan, Jennifer A.. Berliner Institut Für Gesundheitsforschung; Alemania
Fil: Kodra, Dritan. Aristotle University Of Thessaloniki; Grecia
Fil: Kuligowski, Julia. Health Research Institute la Fe; España
Fil: Lan, Renny Shang-Lun. Arkansas Children's Nutrition Center; Estados Unidos
Fil: Monge, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; Argentina
Fil: Moussa, Laura W.. Us Food And Drug Administracion; Estados Unidos
Fil: Nair, Sindhu G.. University of Alberta; Canadá
Fil: Reisdorph, Nichole. University Of Colorado Anschutz Medical Campus.; Estados Unidos
Fil: Sherrod, Stacy D.. Vanderbilt University; Estados Unidos
Fil: Ulmer Holland, Candice. United States Department of Agriculture; Estados Unidos
Fil: Vuckovic, Dajana. Concordia University; Canadá
Fil: Yu, Li-Rong. National Center For Toxicological Research; Estados Unidos. Us Food And Drug Administracion; Estados Unidos
Fil: Zhang, Bo. Olaris Inc; Estados Unidos
Fil: Theodoridis, Georgios. Aristotle University Of Thessaloniki; Grecia
Fil: Mosley, Jonathan D.. Environmental Protection Agency; Estados Unidos