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The Clinical Proteomic Tumor Analysis Consortium (CPTAC) analyzes cancer biospecimens by mass spectrometry, characterizing and quantifying their constituent proteins, or proteome. Mass spectrometry enables highly specific identification of proteins and proteoforms, accurate relative quantitation of protein abundance in contrasting biospecimens, and the localization of post-translational protein modifications, such as phosphorylation, on a protein’s sequence. Read more.

The CPTAC Data Portal is the centralized repository for the dissemination of proteomic data collected by the Proteome Characterization Centers (PCCs) for the CPTAC program. The portal also hosts analyses of the mass spectrometry data (mapping of spectra to peptide sequences and protein identification) from the PCCs and from a CPTAC-sponsored common data analysis pipeline (CDAP). All data is freely available to the public, subject to the data use guidelines.

Data Analysis

Proteomic analysis for each CPTAC study is carried out independently by the PCCs using a variety of protein fractionation techniques, instrumentation, and workflows. The mass spectrometry and related data files are organized into datasets by study, sub-proteome, and analysis site. Currently available sub-proteomes include global (no protein fractionation), phosphoproteome, and glycoproteome. PCCs may also provide higher level analyses of the mass spectrometry raw data computed with their custom bioinformatic pipelines (for example matches of peptides to spectrum and/or protein assemblies). The CPTAC community also supports a Common Data Analysis Pipeline (CDAP) of bioinformatics programs to generate a standard set of data for the public. This CDAP provides the investigators with peptide-spectrum-matches and protein reports for the CPTAC studies.