CPTAC characterized assays are defined as those that meet the criteria described in the Assay Characterization Guidance Document. This guidance document aligns with recommendations by the research community as “fit-for-purpose” validation requirements of targeted proteomics assays.
CPTAC assay characterization process comprises of a set of five experiments, as illustrated in the Schematic Representation of the Assay Characterization Guidance Document designed to help users evaluate assay performance before investing time, money and energy into adopting and deploying these assays in their own laboratories. While Experiments 1 and 2 are required for upload of assays into the portal, additional experiments are highly encouraged although optional. Assays currently residing in the portal are generally comprised of “Tier 2” assays as defined by recommendations for “fit-for-purpose” validation of targeted proteomics assays (Mol Cell Proteomics 2014, PMID 24443746). This guidance document provides assay validation requirements and instructions not only for CPTAC teams, but also for non-CPTAC researchers should they decide to submit their own targeted assays into the portal to help populate this high-quality resource. Guidance document also serves as a resource to authors for publication of manuscripts describing development and application of targeted mass spectrometry measurements of peptides and proteins to the journal Molecular and Cellular Proteomics.