Pan-cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics

CPTAC PAN-cancer Data Repository Welcome to the CPTAC PAN-cancer Data Repository! This repository serves as a data repository for the CPTAC PAN-cancer effort, which focuses on cancer target discovery. It contains various data sets related to protein abundance estimation, derived TMT-TPA, iBAQ, iBAQ-derived copy number, and differential protein expression for CPTAC ten indications. ## Contents The repository includes the following data: - FragPipe Output: Protein abundance estimation data generated using the FragPipe software.<br> - Derived TMT-TPA: Data derived from Tandem Mass Tag (TMT) based Total Protein Approach (TPA).<br> - iBAQ: Data representing intensity-based absolute quantification (iBAQ) of proteins.<br> - iBAQ-derived Copy Number: Data derived from iBAQ analysis for copy number estimation.<br> - Differential Protein Expression: Data indicating differential expression of proteins between tumor and NAT. ## Data Organization The data in this repository is organized in a structured manner to facilitate easy access and navigation. The repository structure is as follows: FragPipe/<br> [fragpipe_data_files]<br> Derived_TMT_TPA/<br> [derived_tmt_tpa_data_files]<br> iBAQ/<br> [ibaq_data_files]<br> iBAQ-derived_copy_number/<br> [ibaq_copy_number_data_files]<br> Differential_protein_expression/<br> [differential_expression_data_files]