While genes are the "recipes" of the cell containing all of the instructions for making molecules called proteins and helping with their assembly, proteins and their modifications by other cellular components, the products of these recipes by tightly controlled mechanisms of transcription and translation, serve as the "engines" to carry out cellular functions and drive both normal and disease physiology.
In the past few years, large-scale multi-disciplinary initiatives such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) have extensively characterized genomic alterations associated with cancer such as copy number aberration, mutation, and microdeletion by multi-dimensional datasets and high level integrative analysis in statistically robust numbers of samples from several types of cancer. These efforts are providing a framework for defining changes in the cancer genome and are setting the stage for the development of molecularly‐based interventions. To extend our knowledge on cancer biology and drive the development of new diagnostics and therapeutics, an understanding of the changes at the protein level that derive from these genomic alterations will be required.
Since proteomics has the capability of characterizing and quantifying proteins and their modifications with state-of-the-art technologies such as mass spectrometry (MS), protein and affinity-based arrays, and bead-based multiplex flow cytometry, it is uniquely positioned to investigate the protein content of a complex biological system. While genomic analysis provides insight into the likelihood of developing cancer or predicting the efficacy of therapeutic intervention, proteins may provide the information to bridge genotype with phenotype in a patient in real time. The resulting proteomic evidence, in this case, will hopefully complement the genomic aberrations in these tumors, and begin to assess the effect of genomic variations on proteins and their intricate networks. Together, these complementary scientific disciplines are absolutely necessary for understanding the molecular underpinnings of disease and for enabling a comprehensive view of what is occurring in cancer.
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) within NCI’s Office of Cancer Clinical Proteomics Research is interrogating the protein content of genomically characterized tumors and accompanying materials in order to link genomics to proteomics. The goal of CPTAC is to systematically analyze proteins, their variations and modifications associated with changes as a result of genomic variations and related biological processes, and to develop public resources for the broad scientific community (e.g. multiplex quantitative assays, datasets of proteins with genomic correlation, and reagents).
CPTAC is composed of a network of Proteome Characterization Centers (PCCs), a Data Center, and a Resource Center. Through the interconnected components, the Office is working together with the external scientific community to further functionalize the genome with proteomic annotation which we hope will lead to improved understanding of cancer.
The Antibody Portal serves as a public resource of monoclonal antibodies made available by the NCI for the scientific community to support protein/peptide measurement and analysis efforts.