The files above allow for running the raw data import, quantitative transition area export and pairwise group comparisons in a fully automated manner with Skyline Batch (SB). The bcfg file contains all necessary parameters. The "Skyline_Batch_Template" Skyline files are used for raw data import, the skyr report for transition area export. Exemplary raw data should yield the provided exemplary analysis output for testing (the raw data folder also contains a csv with the transition area data, in the case that only the R-script but not the full SB-pipeline test is desired). Annotation.txt, ReferenceProtein.csv and SampleList.csv are required by the R-script. For more details and some advice for troubleshooting, see the supplementary material of the manuscript.