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Abstract

Large-scale quantitative mass spectrometry-based metabolomics and proteomics study requires the long-term analysis of multiple batches of biological samples, which often accompanied with significant signal drift and various inter- and intra-batch variations. The unwanted variations can lead to poor inter- and intra-day reproducibility, which is a hindrance to discover real significance. The use of quality control samples and data treatment strategies in the quality assurance procedure provides a mechanism to evaluate the quality and remove the analytical variance of the data. The statTarget we developed is a streamlined tool with an easy-to-use graphical user interface and an integrated suite of algorithms specifically developed for the evaluation of data quality and removal of unwanted variations for quantitative mass spectrometry-based omics data. A novel quality control-based random forest signal correction algorithm, which can remove inter- and intra-batch unwanted variations at feature-level was implanted in the statTarget. Our evaluation based on real samples showed the developed algorithm could improve the data precision and statistical accuracy for mass spectrometry-based metabolomics and proteomics data. Additionally, the statTarget offers the streamlined procedures for data imputation, data normalization, univariate analysis, multivariate analysis, and feature selection. To conclude, the statTarget allows user-friendly the improvement of the data precision for uncovering the biologically differences, which largely facilitates quantitative mass spectrometry-based omics data processing and statistical analysis.