At this stage, the precursor ion masses from the compound lists, their extracted ion chromatograms (EICs, within the specified m/z tolerance) as well as their corresponding MS2 spectral scans are retrieved from the data files. The data is extracted from mzML files using the MSnbase package which enables precise retrieval of extracted ion chromatograms (EICs) and MS2 spectra from mzML files. This is the most time intensive step of the process. The extraction process can be carried out concurrently on multiple files using the future package . This parallelization significantly reduces processing time, particularly for large-scale analyses involving multiple mzML files.