Distilling accurate quantitation information on metabolites from liquid chromatography coupled with mass spectrometry (LC-MS) data sets is crucial for further statistical analysis and biomarker identification. However, it is still challenging due to the complexity of biological systems. The concept of pure ion chromatograms (PICs) is an effective way of extracting meaningful ions, but few toolboxes provide a full processing workflow for LC-MS data sets based on PICs. In this study, an integrated framework, KPIC2, has been developed for metabolomics studies, which can detect pure ions accurately, align PICs across samples, group PICs to identify isotope and potential adducts, fill missing peaks and do multivariate pattern recognition. To evaluate its performance, MM48, metabolomics quantitation, and Soybean seeds data sets have been analyzed using KPIC2, XCMS, and MZmine2. KPIC2 can extract more true ions with fewer detecting features, have good quantification ability on a metabolomics quantitation data set, and achieve satisfactory classification on a soybean seeds data set through kernel-based OPLS-DA and random forest. It is implemented in R programming language, and the software, user guide, as well as example scripts and data sets are available as an open source package at https://github.com/hcji/KPIC2 .