Mass spectrometry (MS)-based metabolomics is a powerful tool for understanding the complexity of biochemical processes and to identify biomarkers across diverse biological systems. The vast amount of data generated by extreme resolution mass spectrometers poses significant data processing challenges, requiring robust computational approaches and workflows for meaningful data interpretation. This chapter provides a comprehensive overview of current methodologies in MS-based metabolomics data analysis, with a focus on data preprocessing and pretreatment, m/z extraction and annotation, univariate and multivariate statistical approaches, as well as data visualization. We discuss key considerations for ensuring data quality and the growing role of bioinformatics in pathway analysis and metabolite identification. We highlight the transforming role of extreme resolution and mass accuracy enabled by FT-ICR mass spectrometers, and finally, we explore emerging trends, including artificial intelligence-driven insights and real-time data processing, to guide future developments in this rapidly evolving field.