PCIS data pre-processing. Raw vendor data files (.wiff) were converted to mzML files using MSConvert (v. 3.0, Proteo Wizard 20 ). A script was developed for peak integration for LC-MS/MS based experiments with PCIS correction. As input, the script requires the mzML files, a list of targets and a list of PCISs with their parameters. Using the target list, the software detects and extracts the MRM signals, followed by resampling and smoothing. It calculates PCIS corrected signals as the scanby-scan ratio of the analyte signal and the PCIS signal, and peak areas as the sum of data points within a specified height of the peak (here set at 99% below maximum). It outputs a data report, including peak areas and PCIS corrected peak areas, as well as pdf-files with chromatograms of before and after correction to enable checking the peak integration and, if necessary, adapting input parameters. The script and a set of demo files have been published in the Github repository github.com/leidenunivlacdr-abs/endoc_pciis. Further data processing was done in Excel (Microsoft).