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Methods Mol Biol. 2016;1410:223-36. doi: 10.1007/978-1-4939-3524-6_13.

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

Author information

1
Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, N., Seattle, WA, 98109, USA.
2
Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA.
3
Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
4
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
5
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
6
Broad Institute, Cambridge, MA, USA.
7
Department of Biochemistry, Jim Ayers Institute for Precancer Detection & Diagnosis, Vanderbilt University School of Medicine, Nashville, TN, USA.
8
Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
9
Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA.
10
Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
11
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
12
Data Coordinating Center, ESAC, Inc., Rockville, MD, USA.
13
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
14
Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
15
Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
16
Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, N., Seattle, WA, 98109, USA. apaulovi@fredhutch.org.

Abstract

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 posttranslational 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.

KEYWORDS:

Harmonization; MRM; Multiple reaction monitoring; PRM; Quantitative assay database; Quantitative proteomics; SRM; Selected reaction monitoring; Standardization; Targeted mass spectrometry

PMID:
26867747
PMCID:
PMC5017244
DOI:
10.1007/978-1-4939-3524-6_13
[Indexed for MEDLINE]
Free PMC Article

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