QComics: Recommendations and Guidelines for Robust, Easily Implementable and Reportable Quality Control of Metabolomics Data

Abstract

The implementation of quality control strategies is crucial to ensure the reproducibility, accuracy, and meaningfulness of metabolomics data. However, this pivotal step is often overlooked within the metabolomics workflow and frequently relies on the use of nonstandardized and poorly reported protocols. To address current limitations in this respect, we have developed QComics, a robust, easily implementable and reportable method for monitoring and controlling data quality. The protocol operates in various sequential steps aimed to (i) correct for background noise and carryover, (ii) detect signal drifts and "out-of-control" observations, (iii) deal with missing data, (iv) remove outliers, (v) monitor quality markers to identify samples affected by improper collection, preprocessing, or storage, and (vi) assess overall data quality in terms of precision and accuracy. Notably, this tool considers important issues often neglected along quality control, such as the need of separately handling missing values and truly absent data to avoid losing relevant biological information, as well as the large impact that preanalytical factors may elicit on metabolomics results. Altogether, the guidelines compiled in QComics might contribute to establishing gold standard recommendations and best practices for quality control within the metabolomics community.

Challenges and recent advances in quantitative mass spectrometry‐based metabolomics

“…For further information, the readers are referred to more detailed studies focusing on these aspects. 26 , 27 , 28 , 29 , 30 , 31 , 32 …”

PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data

“…While there are active community efforts to establish and promote best practices for QC in untargeted metabolomics, − the number of available software tools for QC in metabolomics is limited. Traditional QC approaches often involve manual inspection of the spectra, which is time-consuming, subjective, and prone to human error.…”