Evidence map›Paper›PMID 26719571›Full record

ArticleClinical chemistry2016

Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays.

Andrew N Hoofnagle, Jeffrey R Whiteaker, Steven A Carr, Eric Kuhn, Tao Liu, Sam A Massoni, Stefani N Thomas, R Reid Townsend, Lisa J Zimmerman, Emily Boja and 45 more

Abstract read
In one paragraph

Article in Clinical chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers.

0numbers the graph read from it
0cells of the map it votes in
107citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

107 citing papers in PubMed.

  1. Article
  2. Article
  3. Proteomic approaches for interrogating kinase signaling networks.The Journal of investigative dermatology · 2026
    Article
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  9. Review
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  12. Review
  13. Article
  14. Article
  15. Article
  16. Frontiers in bioinformatics · 2025
    Article
  17. Article
  18. Article
  19. Article
  20. Article

47 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

55 authors.

Andrew N HoofnagleUniversity of Washington, Seattle, WA; ahoof@u.washington.edu apaulovi@fhcrc.org.
Jeffrey R WhiteakerFred Hutchinson Cancer Research Center, Seattle, WA;
Steven A CarrBroad Institute, Cambridge, MA;
Eric KuhnBroad Institute, Cambridge, MA;
Tao LiuPacific Northwest National Laboratory, Richland, WA;
Sam A MassoniNew England Peptide, Inc., Gardner, MA;
Stefani N ThomasJohns Hopkins University, Baltimore, MD;
R Reid TownsendWashington University, St Louis, MO;
Lisa J ZimmermanVanderbilt University, Nashville, TN;
Emily BojaNational Cancer Institute, Bethesda, MD;
Jing ChenJohns Hopkins University, Baltimore, MD;
Daniel L CrimminsWashington University, St Louis, MO;
Sherri R DaviesWashington University, St Louis, MO;
Yuqian GaoPacific Northwest National Laboratory, Richland, WA;
Tara R HiltkeNational Cancer Institute, Bethesda, MD;
Karen A KetchumESAC, Inc., Rockville, MD;
Christopher R KinsingerNational Cancer Institute, Bethesda, MD;
Mehdi MesriNational Cancer Institute, Bethesda, MD;
Matthew R MeyerWashington University, St Louis, MO;
Wei-Jun QianPacific Northwest National Laboratory, Richland, WA;
Regine M SchoenherrFred Hutchinson Cancer Research Center, Seattle, WA;
Mitchell G ScottWashington University, St Louis, MO;
Tujin ShiPacific Northwest National Laboratory, Richland, WA;
Gordon R WhiteleyFrederick National Laboratory for Cancer Research, Frederick, MD;
John A WrobelUniversity of North Carolina School of Medicine, Chapel Hill, NC;
Chaochao WuPacific Northwest National Laboratory, Richland, WA;
Brad L AckermannEli Lilly and Company, Indianapolis, IN;
Ruedi AebersoldInstitute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland;
David R BarnidgeMayo Clinic College of Medicine, Rochester, MN;
David M BunkNIST, Gaithersburg, MD;
Nigel ClarkeQuest Diagnostics, San Juan Capistrano, CA;
Jordan B Fishman21st Century Biochemicals, Inc., Marlborough, MA;
Russ P GrantLaboratory Corporation of America Holdings, Inc., Burlington, NC;
Ulrike KusebauchInstitute for Systems Biology, Seattle, WA;
Mark M KushnirUniversity of Utah and ARUP Laboratories, Salt Lake City, UT;
Mark S LowenthalNIST, Gaithersburg, MD;
Robert L MoritzInstitute for Systems Biology, Seattle, WA;
Hendrik NeubertPfizer, Inc., Andover, MA;
Scott D PattersonGilead Sciences, Inc., Foster City, CA;
Alan L RockwoodUniversity of Utah and ARUP Laboratories, Salt Lake City, UT;
John RogersThermo Fisher Scientific, Rockford, IL;
Ravinder J SinghMayo Clinic College of Medicine, Rochester, MN;
Jennifer E Van EykCedars Sinai Medical Center, Los Angeles, CA;
Steven H WongWake Forest School of Medicine, Winston-Salem, NC;
Shucha ZhangEnanta Pharmaceuticals, Watertown, MA;
Daniel W ChanJohns Hopkins University, Baltimore, MD;
Xian ChenUniversity of North Carolina School of Medicine, Chapel Hill, NC;
Matthew J EllisBaylor College of Medicine, Houston, TX.
Daniel C LieblerVanderbilt University, Nashville, TN;
Karin D RodlandPacific Northwest National Laboratory, Richland, WA;
Henry RodriguezNational Cancer Institute, Bethesda, MD;
Richard D SmithPacific Northwest National Laboratory, Richland, WA;
Zhen ZhangJohns Hopkins University, Baltimore, MD;
Hui ZhangJohns Hopkins University, Baltimore, MD;
Amanda G PaulovichFred Hutchinson Cancer Research Center, Seattle, WA; ahoof@u.washington.edu apaulovi@fhcrc.org.

Funding

Washington University Center for Cellular ImagingP30CA091842 · NCI · WASHINGTON UNIVERSITY · PI TIMOTHY J. EBERLEIN · 2001 to 2026
$128.0M
Quantitative Systems BiologyP50GM076547 · NIGMS · INSTITUTE FOR SYSTEMS BIOLOGY · PI BALIGA, NITIN S · 2006 to 2016
$30.6M
Proteo-genomic Discovery, Prioritization and Verification of Cancer BiomarkersU24CA160034 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, PAULOVICH, AMANDA G · 2011 to 2016
$16.2M
PNNL Clinical Proteome Characterization CenterU24CA160019 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI RODLAND, KARIN D, SMITH, RICHARD D · 2011 to 2016
$15.7M
Vanderbilt Proteome Characterization CenterU24CA159988 · NCI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI LIEBLER, DANIEL C · 2011 to 2016
$13.9M
Cancer Proteome Center at Washington Univ, Univ of North Carolina & Boise StateU24CA160035 · NCI · WASHINGTON UNIVERSITY · PI CHEN, XIAN, ELLIS, MATTHEW J · 2011 to 2016
$11.8M
Proteome Characterization Center: A Genoproteomics Pipeline for Cance ResearchU24CA160036 · NCI · JOHNS HOPKINS UNIVERSITY · PI CHAN, DANIEL WANYUI, ZHANG, HUI · 2011 to 2016
$10.7M
Clinical and Analytical Validation of Cancer BiomarkersU24CA115102 · NCI · JOHNS HOPKINS UNIVERSITY · PI CHAN, DANIEL WANYUI · 2005 to 2021
$7.4M
Shortening the development cycle time of Trans Proteomic Pipeline tools with high performance computingR01GM087221 · NIGMS · INSTITUTE FOR SYSTEMS BIOLOGY · PI DEUTSCH, ERIC, MORITZ, ROBERT L · 2010 to 2021
$6.0M
Proteomic Approach to CKD Biomarker Discovery and ValidationU01DK085689 · NIDDK · JOHNS HOPKINS UNIVERSITY · PI CORESH, JOSEF · 2009 to 2019
$5.6M
Mechanisms underlying therapy failure of immune checkpoint inhibitors and Notch1 loss-mediated immunosuppression in head and neck cancersF31DE027854 · NIDCR · UNIVERSITY OF COLORADO DENVER · PI WOOLAVER, RACHEL A · 2018 to 2020
$100k
NCI NIH HHS P30 CA091842NCI NIH HHS U24CA115102NCI NIH HHS U24CA159988NCI NIH HHS U24 CA160019NCI NIH HHS U24CA160019NCI NIH HHS U24 CA160034NCI NIH HHS U24CA160034NCI NIH HHS U24 CA160035NCI NIH HHS U24CA160035NCI NIH HHS U24CA160036NIDCR NIH HHS F31 DE027854NIDDK NIH HHS U01DK085689NIGMS NIH HHS P50GM076547NIGMS NIH HHS R01 GM087221NIGMS NIH HHS R01GM087221
6 · The paper itself

Abstract

backgroundFor many years, basic and clinical researchers have taken advantage of the analytical sensitivity and specificity afforded by mass spectrometry in the measurement of proteins. Clinical laboratories are now beginning to deploy these work flows as well. For assays that use proteolysis to generate peptides for protein quantification and characterization, synthetic stable isotope-labeled internal standard peptides are of central importance. No general recommendations are currently available surrounding the use of peptides in protein mass spectrometric assays. CONTENT: The Clinical Proteomic Tumor Analysis Consortium of the National Cancer Institute has collaborated with clinical laboratorians, peptide manufacturers, metrologists, representatives of the pharmaceutical industry, and other professionals to develop a consensus set of recommendations for peptide procurement, characterization, storage, and handling, as well as approaches to the interpretation of the data generated by mass spectrometric protein assays. Additionally, the importance of carefully characterized reference materials-in particular, peptide standards for the improved concordance of amino acid analysis methods across the industry-is highlighted. The alignment of practices around the use of peptides and the transparency of sample preparation protocols should allow for the harmonization of peptide and protein quantification in research and clinical care.

Indexed as

Clinical Laboratory TechniquesMass SpectrometryProteomicsSpecimen HandlingGuidelines as TopicHumansPeptidesResearch PersonnelPeptides

Identifiers

PMID26719571
PMCPMC4830481

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.