title: Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.
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.
authors: Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, N., Seattle, WA, 98109, USA.
authors: Jeffrey R
authors: JR
authors: Whiteaker
authors: Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA.
authors: Goran N
authors: GN
authors: Halusa
authors: Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
authors: Andrew N
authors: AN
authors: Hoofnagle
authors: Department of Genome Sciences, University of Washington, Seattle, WA, USA.
authors: Vagisha
authors: V
authors: Sharma
authors: Department of Genome Sciences, University of Washington, Seattle, WA, USA.
authors: Brendan
authors: B
authors: MacLean
authors: Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, N., Seattle, WA, 98109, USA.
authors: Ping
authors: P
authors: Yan
authors: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
authors: John A
authors: JA
authors: Wrobel
authors: Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, N., Seattle, WA, 98109, USA.
authors: Jacob
authors: J
authors: Kennedy
authors: Broad Institute, Cambridge, MA, USA.
authors: D R
authors: DR
authors: Mani
authors: Department of Biochemistry, Jim Ayers Institute for Precancer Detection & Diagnosis, Vanderbilt University School of Medicine, Nashville, TN, USA.
authors: Lisa J
authors: LJ
authors: Zimmerman
authors: Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
authors: Matthew R
authors: MR
authors: Meyer
authors: Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA.
authors: Mehdi
authors: M
authors: Mesri
authors: Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA.
authors: Emily
authors: E
authors: Boja
authors: Broad Institute, Cambridge, MA, USA.
authors: Steven A
authors: SA
authors: Carr
authors: Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors: Daniel W
authors: DW
authors: Chan
authors: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
authors: Xian
authors: X
authors: Chen
authors: Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors: Jing
authors: J
authors: Chen
authors: Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
authors: Sherri R
authors: SR
authors: Davies
authors: Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
authors: Matthew J C
authors: MJ
authors: Ellis
authors: Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
authors: David
authors: D
authors: Fenyö
authors: Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA.
authors: Tara
authors: T
authors: Hiltke
authors: Data Coordinating Center, ESAC, Inc., Rockville, MD, USA.
authors: Karen A
authors: KA
authors: Ketchum
authors: Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA.
authors: Chris
authors: C
authors: Kinsinger
authors: Broad Institute, Cambridge, MA, USA.
authors: Eric
authors: E
authors: Kuhn
authors: Department of Biochemistry, Jim Ayers Institute for Precancer Detection & Diagnosis, Vanderbilt University School of Medicine, Nashville, TN, USA.
authors: Daniel C
authors: DC
authors: Liebler
authors: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
authors: Tao
authors: T
authors: Liu
authors: Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA.
authors: Michael
authors: M
authors: Loss
authors: Department of Genome Sciences, University of Washington, Seattle, WA, USA.
authors: Michael J
authors: MJ
authors: MacCoss
authors: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
authors: Wei-Jun
authors: WJ
authors: Qian
authors: Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA.
authors: Robert
authors: R
authors: Rivers
authors: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
authors: Karin D
authors: KD
authors: Rodland
authors: Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
authors: Kelly V
authors: KV
authors: Ruggles
authors: Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
authors: Mitchell G
authors: MG
authors: Scott
authors: Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
authors: Richard D
authors: RD
authors: Smith
authors: Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors: Stefani
authors: S
authors: Thomas
authors: Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
authors: R Reid
authors: RR
authors: Townsend
authors: Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA.
authors: Gordon
authors: G
authors: Whiteley
authors: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
authors: Chaochao
authors: C
authors: Wu
authors: Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors: Hui
authors: H
authors: Zhang
authors: Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors: Zhen
authors: Z
authors: Zhang
authors: Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA.
authors: Henry
authors: H
authors: Rodriguez
authors: Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, N., Seattle, WA, 98109, USA. apaulovi@fredhutch.org.
authors: Amanda G
authors: AG
authors: Paulovich
mesh_terms: D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D010455:Peptides / Q000032:analysis; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods*
chemical_list: D010455:Peptides; D011506:Proteins
keywords: Harmonization; MRM; Multiple reaction monitoring; PRM; Quantitative assay database; Quantitative proteomics; SRM; Selected reaction monitoring; Standardization; Targeted mass spectrometry