This repository contains the analysis pipeline for the manuscript: "Proteomic Characterization of Intrahepatic Cholangiocarcinoma Identifies Risk-Stratifying Subgroups, Proteins Associated with Time-To-Recurrence, and mTOR Effector Molecule EIF4A1 as a Druggable Therapeutic Target." The study is based on proteomic data from a human cohort of intrahepatic cholangiocarcinoma (ICC) comprising 80 tumor and 77 tumor-adjacent, non-malignant (TANM) tissue samples from 80 patients. All samples were measured on a TimsTOF Flex coupled to an Evosep One chromatographic system. Data from earlier measurements on a Thermo QExactive coupled to an Easynlc nanoflow system is available but was not included in the publication. The cohort was analyzed using DIA-NN 1.9.2 with a fully tryptic database, and a semi-specific database to study proteolytic events. Additionally, we analyzed 9 patient-derived ICC xenografts (PDX). This release corresponds to the version used in the manuscript