1 Analytical Resources Core: Bioanalysis and Omics Center; Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80525, United States.
2 Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, United States.
3 Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States.
4 Department of Oncology, Hospital Universitari Sant Joan de Reus, Institut d'Investigació Sanitària Pere Virgili (IISPV), URV, CERCA, 43204 Reus, Spain.
5 Agilent Technologies Inc., 5301 Stevens Creek Blvd, Santa Clara, California 95051, United States.
6 Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota 55905, United States.
7 National Institute of Standards and Technology, Chemical Sciences Division, 331 Fort Johnson Road, Charleston, South Carolina 29412, United States.
8 Centre for Metabolomics Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown St., Liverpool L69 7ZB,U.K.
9 Metabolon, Inc. 617 Davis Drive, Suite 100, Morrisville, North Carolina 27560, United States.
10 Department of Analytical Chemistry, University of Granada, 18071 Granada, Spain.
11 School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
12 Metabolon, Inc., 617 Davis Drive, Suite 100, Morrisville, North Carolina 27560, United States.
13 Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Gudelsky Drive, Rockville, Maryland 20850, United States.
14 Department of Environmental Health Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7190, United States.
15 Metabolomics, Berlin Institute of Health at Charite, Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany.
16 Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
17 Neonatal Research Group, Health Research Institute La Fe, Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain.
18 Arkansas Children's Nutrition Center, Little Rock, Arkansas 72202-3591, United States.
19 Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina.
20 Center for Veterinary Medicine, Office of New Animal Drug Evaluation, U.S. Food and Drug Administration, Rockville, Maryland 20855, United States.
21 Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2G2, Canada.
22 Department of Pharmaceutical Sciences, University of Colorado-Anschutz Medical Campus, Aurora, Colorado 80045, United States.
23 Department of Chemistry and Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37240, United States.
24 Chemistry Branch, Eastern Laboratory, Office of Public Health Science, USDA-FSIS, Athens, Georgia 30605, United States.
25 Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada.
26 Olaris, Inc., 175 Crossing Blvd Suite 410, Framingham, Massachusetts 01702, United States.
27 Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Gre

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.