This package provides a multi-layered untargeted pipeline for high-throughput LC/HRMS data processing to extract signals of organic small molecules. The package performs ion pairing, peak detection, peak table alignment, retention time correction, aligned peak table gap filling, peak annotation and visualization of extracted ion chromatograms (EICs) and total ion chromatograms (TICs). The IDSL.IPA package was introduced in <doi:10.1021/acs.jproteome.2c00120> .