MRMkit is an open-source software package designed for automated processing of large-scale targeted mass spectrometry-based metabolomics data. With improvements in the automation of sample preparation for LC-MS analysis, a challenging next step is to fully automate the workflow to process raw data and ensure the quality of measurements in large-scale analysis settings. MRMkit capitalizes on the richness of large-sample data in capturing peak shapes and interference patterns of transitions across many samples and delivers fully automated, reproducible peak integration results in a scalable and time-efficient manner. In addition to fast and accurate peak integration, the tool also provides reliable data normalization functions and quality metrics along with visualizations for fast data quality evaluation. In addition, MRMkit learns retention time offset patterns by user-specified compound classes and makes recommendations for peak picking in multimodal ion chromatograms. In summary, MRMkit offers highly consistent and scalable data processing capacity for targeted metabolomics, substantially curtailing the time required to produce the final quantification results after LC-MS analysis.