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

  • Jeffrey R. Whiteaker
  • Goran N. Halusa
  • Andrew N. Hoofnagle
  • Vagisha Sharma
  • Brendan MacLean
  • Ping Yan
  • John A. Wrobel
  • Jacob Kennedy
  • D. R. Mani
  • Lisa J. Zimmerman
  • Matthew R. Meyer
  • Mehdi Mesri
  • Emily Boja
  • Steven A. Carr
  • Daniel W. Chan
  • Xian Chen
  • Jing Chen
  • Sherri R. Davies
  • Matthew J. C. Ellis
  • David Fenyö
  • Tara Hiltke
  • Karen A. Ketchum
  • Chris Kinsinger
  • Eric Kuhn
  • Daniel C. Liebler
  • Tao Liu
  • Michael Loss
  • Michael J. MacCoss
  • Wei-Jun Qian
  • Robert Rivers
  • Karin D. Rodland
  • Kelly V. Ruggles
  • Mitchell G. Scott
  • Richard D. Smith
  • Stefani Thomas
  • R. Reid Townsend
  • Gordon Whiteley
  • Chaochao Wu
  • Hui Zhang
  • Zhen Zhang
  • Henry Rodriguez
  • Amanda G. PaulovichEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1410)

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.

Key words

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

Notes

Acknowledgements

This work was funded by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the US National Cancer Institute (U24CA160034, U24CA160036, U24CA160019, U24CA159988, and U24CA160035), R01 GM103551, and U01 CA164186.

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • 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
  • Emily Boja
    • 9
  • Steven A. Carr
    • 6
  • Daniel W. Chan
    • 10
  • Xian Chen
    • 5
  • Jing Chen
    • 10
  • Sherri R. Davies
    • 8
  • Matthew J. C. Ellis
    • 8
  • David Fenyö
    • 11
  • Tara Hiltke
    • 9
  • Karen A. Ketchum
    • 12
  • Chris Kinsinger
    • 9
  • Eric Kuhn
    • 6
  • Daniel C. Liebler
    • 7
  • Tao Liu
    • 13
  • Michael Loss
    • 2
  • Michael J. MacCoss
    • 4
  • Wei-Jun Qian
    • 13
  • Robert Rivers
    • 9
  • Karin D. Rodland
    • 13
  • Kelly V. Ruggles
    • 11
  • Mitchell G. Scott
    • 14
  • Richard D. Smith
    • 15
  • Stefani Thomas
    • 10
  • R. Reid Townsend
    • 8
  • Gordon Whiteley
    • 2
  • Chaochao Wu
    • 13
  • Hui Zhang
    • 10
  • Zhen Zhang
    • 10
  • Henry Rodriguez
    • 9
  • Amanda G. Paulovich
    • 1
    Email author
  1. 1.Clinical Research DivisionFred Hutchinson Cancer Research CenterSeattleUSA
  2. 2.Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research Inc.FrederickUSA
  3. 3.Department of Laboratory MedicineUniversity of WashingtonSeattleUSA
  4. 4.Department of Genome SciencesUniversity of WashingtonSeattleUSA
  5. 5.Department of Biochemistry and BiophysicsUniversity of North Carolina at Chapel Hill School of MedicineChapel HillUSA
  6. 6.Broad InstituteCambridgeUSA
  7. 7.Department of Biochemistry, Jim Ayers Institute for Precancer Detection & DiagnosisVanderbilt University School of MedicineNashvilleUSA
  8. 8.Department of MedicineWashington University School of MedicineSt. LouisUSA
  9. 9.Office of Cancer Clinical Proteomics ResearchNational Cancer InstituteBethesdaUSA
  10. 10.Clinical Chemistry Division, Department of PathologyJohns Hopkins University School of MedicineBaltimoreUSA
  11. 11.Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUSA
  12. 12.Data Coordinating Center, ESAC, Inc.RockvilleUSA
  13. 13.Biological Sciences DivisionPacific Northwest National LaboratoryRichlandUSA
  14. 14.Division of Laboratory and Genomic Medicine, Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUSA
  15. 15.Biological Sciences Division and Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandUSA

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