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Non-targeted and suspect screening analysis using liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) holds great promise to comprehensively characterize complex chemical mixtures. Data preprocessing is a crucial part of the process, however, some limitations are observed: (i) peak-picking and feature extraction might be incomplete, especially for low abundant compounds, and (ii) limited reproducibility has been observed between laboratories and software for detected features and their relative quantification. We first conducted a critical review of existing solutions that could improve the reproducibility of preprocessing for LC-HRMS. Solutions include providing repositories and reporting guidelines, open and modular processing workflows, public benchmark datasets, tools to optimize the data preprocessing and to filter out false positive detections. We then propose harmonized quality assurance/quality control guidelines that would allow to assess the sensitivity of feature detection, reproducibility, integration accuracy, precision, accuracy, and consistency of data preprocessing for human biomonitoring, food and environmental communities. • Preprocessing of raw data from SS and NTA by (LC-HRMS) is affected by reproducibility and incomplete peak peaking. • Optimization tools and guidelines were developed to improve SSA/NTA LC-HRMS data preprocessing. • QA/QC provisions for SSA/NTS LC-HRMS data preprocessing are proposed to assess performance of preprocessing. [ABSTRACT FROM AUTHOR]