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. 2014 Jul;11(7):703-4.
doi: 10.1038/nmeth.3002.

CPTAC Assay Portal: a repository of targeted proteomic assays

Jeffrey R Whiteaker  1 , Goran N Halusa  2 , Andrew N Hoofnagle  3 , Vagisha Sharma  4 , Brendan MacLean  4 , Ping Yan  1 , John A Wrobel  5 , Jacob Kennedy  1 , D R Mani  6 , Lisa J Zimmerman  7 , Matthew R Meyer  8 , Mehdi Mesri  9 , Henry Rodriguez  9 ; Clinical Proteomic Tumor Analysis Consortium (CPTAC); Amanda G Paulovich  1
Collaborators, Affiliations

CPTAC Assay Portal: a repository of targeted proteomic assays

Jeffrey R Whiteaker et al. Nat Methods. 2014 Jul.
No abstract available

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Figures

Figure 1
Figure 1
Overview of the CPTAC assay portal. (a) The CPTAC Assay Portal enables query of a database of well-characterized, targeted MS-based assays. Bioinformatic annotations are pulled from outside sources to enable biologically relevant queries, as well as mapping of peptide analytes relative to sequence domains, isoforms, coding polymorphisms and post-translational modifications. Contributions from external sites are noted on the portal. The assay database is tied to Panorama, an open-source platform allowing for efficient collection and sharing of proteomics data in a vendor-neutral format (for example, currently supporting data from six vendors: AB SCIEX, Agilent, Bruker, Shimadzu, Thermo and Waters), facilitating upload and viewing of assay characterization data, and download of Skyline documents for implementing the assays. (b) CPTAC characterization is a set of experiments designed to help users evaluate assay performance. There are five recommended experiments. Experiments 1 and 2 are required for each assay; experiments 3–5 are optional. Experiment 1 is a response curve (dilution curve of peptides spiked into a representative background matrix) designed to evaluate linearity, the within-batch precision of the liquid chromatography–MRM-MS analysis of the analyte peptide in a complex mixture and the upper and lower limits of quantification, and to provide data on selectivity (through detection of interferences in the curve data). Experiment 2 (evaluation of repeatability, three replicates of peptides spiked at three concentrations—low, medium (mid) and high) determines the repeatability of measurements at multiple concentrations across 5 d. Experiment 3 tests selectivity by evaluating parallelism (a measure of the influence of matrix components on the quantification of peptides in a complex mixture) in multiple biological replicates of the matrix of interest. Experiment 4 evaluates the stability of peptides after sample preparation and helps the downstream user determine whether peptides can be left on the autosampler for a period of time or frozen before analysis. Experiment 5 aims to demonstrate that endogenous peptides can be quantified in a relevant matrix. y4, y5, y6, and Sum denote the transition ion plotted in each graph.
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