Algorithms and tools for the preprocessing of LC–MS metabolomics data

Metabolomics encompasses the study of small molecules in a biological sample. Liquid Chromatography coupled with Mass Spectrometry (LC–MS) profiling is an important approach for the identification and quantification of metabolites from complex biological samples. The amount and complexity of data produced in an LC–MS profiling experiment demand automatic tools for the preprocessing, analysis, and extraction of useful biological information. Data preprocessing—a topic that covers noise filtering, peak detection, deisotoping, alignment, identification, and normalization—is thus an active area of metabolomics research. Recent years have witnessed development of many software for data preprocessing, and still there is a need for further improvement of the data preprocessing pipeline. This review presents an overview of selected software tools for preprocessing LC–MS based metabolomics data and tries to provide future directions.