A system suitability testing platform for untargeted, high-resolution mass spectrometry

Dmitrenko, Andrei; Reid, Michelle; Zamboni, Nicola

doi:10.3389/fmolb.2022.1026184

Cited by 2 publications

(2 citation statements)

References 19 publications

(20 reference statements)

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“…There are clear opportunities for the community to increase the use of pooled QC samples in improving data quality, especially considering that the pooled QC samples are frequently being generated and analyzed with the full data set. A recent publication offers guidance on pooled QC usage and reporting, 2 in which readers can find specific recommendations surrounding pooled QC usage.…”

Section: Discussionmentioning

confidence: 99%

“…These characteristics make LC-MS appealing, but LC-MS is also susceptible to batch effects and background interferences. Quality control (QC) processes are especially challenging for untargeted analytical approaches, including metabolomics. , Coordinated efforts to emphasize quality management measures have emerged in recent years. However, quality management protocols in the field of metabolomics have been slow to gain community-wide acceptance, in part due to a lack of standardization as it relates to sample type, MS ionization conditions, LC mobile phase solvent composition, column chemistry, and gradient, among other experimental conditions.…”

Section: Introductionmentioning

confidence: 99%

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

Broeckling,

Beger,

Cheng

et al. 2023

Anal. Chem.

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%