CPTAC Assay Portal: a community web-based repository for well-characterized quantitative targeted proteomics assays

A rapidly growing trend in protein quantification is using targeted mass spectrometry (MS). Although hundreds of MS-based assays have been published, the information is dispersed throughout the literature, protocols for characterization of assay performances have not been standardized, and there is currently no public database of analytically validated assays and standard operating protocols (SOPs), which are critical for standardizing and harmonizing proteomic results across the community. As a result, despite the widespread capability to perform techniques like multiple reaction monitoring (MRM) in modern proteomic facilities, the benefits of MRM have not yet been fully realized by the wider biological and clinical research communities.

To address these issues, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as a public repository of well-characterized quantitative, targeted proteomic assays. The purpose of the CPTAC Assay Portal is to facilitate widespread adoption of targeted MS assays by disseminating SOPs, reagents, and assay characterization data. A primary aim of the portal is to bring together clinicians or biologists and analytical chemists to answer hypothesis-driven questions using targeted, MS-based assays. Assay content is accessed through queries and filters, enabling investigators to find assays to proteins involved in specific cellular pathways or protein complexes, proteins whose genes map to specific chromosomal regions, or proteins associated with specified Gene Ontologies. Assays are displayed using a protein-centric view onto which the position of peptide analytes are mapped relative to features of interest, such as sequence domains, isoforms, single nucleotide polymorphisms, and post-translational modifications. Finally, detailed characterization data (linked to the portal through Panorama, https://panoramaweb.org) are available for each assay, enabling researchers to evaluate performance prior to launching the assay in their own laboratory.