Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays

Abstract

Summary 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 an open-source repository of well-characterized targeted proteomic assays. The portal is designed to curate and disseminate highly characterized, targeted mass spectrometry (MS)-based assays by providing detailed assay performance characterization data, standard operating procedures, and access to reagents. Assay content is accessed via the portal through queries to find assays targeting proteins associated with specific cellular pathways, protein complexes, or specific chromosomal regions. The position of the peptide analytes for which there are available assays are mapped relative to other features of interest in the protein, such as sequence domains, isoforms, single nucleotide polymorphisms, and post-translational modifications. The overarching goals are to enable robust quantification of all human proteins and to standardize the quantification of targeted MS-based assays to ultimately enable harmonization of results over time and across laboratories.

Multiplexed MRM-based protein quantification of putative prognostic biomarkers for chronic kidney disease progression in plasma

“…To perform the selection, multiple tools were employed in combination: a spectral library from the National Institute of Standards and Technology (NIST) ["human consensus final true lib", downloaded from http://www.nist.gov/] on 05062014] was imported into Skyline software. The Skyline indicated proteotypic peptides and respective transitions per peptide which were further validated with additional bioinformatics tools: The PeptidePicker (http://mrmpeptidepicker.proteincentre.com/peptidepicker9/) that predicts proteotypic peptides with similar criteria as Skyline 85 ; The Peptide Tracker (http://tracker.proteincentre.com/) that records transitions and chromatographic properties of specific proteotypic peptides based on previously performed MRM assays 86 , and the CPTAC Assay Portal (https://assays.cancer.gov/available_assays) that compiles information of existing MRM assays (proteotypic peptides, analytical performance, suggested protocols) 87 . In addition, shortlisted peptides were evaluated using the Protein Basic Local Alignment Search Tool (BLAST, http://blast.ncbi.nlm.nih.gov) to ensure their proteotypicity.…”

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

“…Many useful resources for developing sensitive and specific SRM assays can be found, for example, in SRM Atlas [8] or at the CPTAC Portal [9,10] as recently reviewed [11]. Kusebauch et al have synthesized and measured 166,174 proteotypic peptides, and this data is now available in SRM Atlas to aid in development of targeted SRM assays for quantification of 99.7% of the 20,277 annotated human proteins [12].…”

Towards comprehensive and quantitative proteomics for diagnosis and therapy of human disease

“…This can also involve knowledge-based "sentinel" proteins [61], or other markers of pathway activity, such as those generated by reduced representation approaches [62]. Collections of SRM assays for this purpose have already begun development for cancer and infectious diseases [63][64][65][66].…”