Proteomic Assays

The Proteomic Assay Portal serves as a centralized public repository of "fit-for-purpose," multiplexed quantitative mass spectrometry-based, proteomic targeted assays. Targeted proteomic assays have been designed to eliminate issues that are common with conventional protein detection systems.

The goal of the portal is to widely disseminate highly characterized proteomic assays to the global research community. We also give researchers access to SOPs and assay characterization/validation data in accordance with the National Institutes of Health’s Rigor and Reproducibility Principles and Guidelines. Targeted mass spectrometry assays are characterized according to the CPTAC assay characterization guidelines.

The portal is also designed for biologists who are seeking to ask hypothesis-driven questions about the proteome they study. It allows them to work with analytical chemists who are equipped to perform targeted proteomic assays. The guidance document provided aligns with recommendations by the research community as “fit-for-purpose” validation requirements of targeted proteomics assays. 

View Available Assays

Assay Development Process

Typical steps involved in the development of a mass spectrometry-based targeted assay include:

1. Selection of surrogate or signature peptides corresponding to the targeted protein or modification of interest;
2. Iterative optimization of instrument and method parameters for optimal detection of the selected peptide;
3. Method development for protein extraction from biological matrices such as tissue, whole cell lysates, or blood plasma/serum and for proteolytic digestion of proteins (usually with trypsin);
4. Evaluation of the assay in the intended biological matrix to determine if the endogenous analyte is detected; if target analytes are of low abundance, an enrichment step may be necessary; and
5. Assay validation, which involves applying fit-for-purpose principles on biological samples to characterize assay performance.

The incorporation of standard operating procedures (SOPs) and method documentation are critical for maintaining the reproducibility and transferability of measurements. Bioinformatic support for such an endeavor is critical in assay configuration and data analysis. Publicly available software/algorithms and peptide/protein databases that are useful for successfully configuring targeted mass spectrometry-based assays include: Skyline, PeptideAtlas, SRMAtlas, PRIDE, and others. Once developed and characterized, these assays can readily be deployed and adopted across laboratories for the precise quantification of the targeted peptide/protein.

Collaboration Opportunities

NCI’s OCCPR seeks collaboration with interested parties to accelerate the uptake of proteomic assays and technologies. The program aims to enable basic and clinical studies, and ultimately to translate the results into advances in patient care. There are many opportunities for collaboration with the NCI in areas of assay development, validation and dissemination. Find more information on collaborative opportunities by emailing us (cancer.proteomics@mail.nih.gov).