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.
- Derived TMT-TPA: Data derived from Tandem Mass Tag (TMT) based Total Protein Approach (TPA).
- iBAQ: Data representing intensity-based absolute quantification (iBAQ) of proteins.
- iBAQ-derived Copy Number: Data derived from iBAQ analysis for copy number estimation.
- 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/
[fragpipe_data_files]
Derived_TMT_TPA/
[derived_tmt_tpa_data_files]
iBAQ/
[ibaq_data_files]
iBAQ-derived_copy_number/
[ibaq_copy_number_data_files]
Differential_protein_expression/
[differential_expression_data_files]