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, Jing Chen, Daniel L. Crimmins, Sherri R. Davies, Yuqian Gao, Tara R. Hiltke, Karen A. Ketchum, Christopher R. Kinsinger, Mehdi Mesri, Matthew R. Meyer, Wei Jun Qian & 35 others Regine M. Schoenherr, Mitchell G. Scott, Tujin Shi, Gordon R. Whiteley, John A. Wrobel, Chaochao Wu, Brad L. Ackermann, Ruedi Aebersold, David R. Barnidge, David M. Bunk, Nigel Clarke, Jordan B. Fishman, Russ P. Grant, Ulrike Kusebauch, Mark M. Kushnir, Mark S. Lowenthal, Robert L. Moritz, Hendrik Neubert, Scott D. Patterson, Alan L. Rockwood, John Rogers, Ravinder J. Singh, Jennifer E. Van Eyk, Steven H. Wong, Shucha Zhang, Daniel Wan-Yui Chan, Xian Chen, Matthew J. Ellis, Daniel C. Liebler, Karin D. Rodland, Henry Rodriguez, Richard D. Smith, Zhen Zhang, Hui Zhang, Amanda G. Paulovich

Research output: Contribution to journalArticle

Abstract

BACKGROUND: For 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 isotopelabeled 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.

Original languageEnglish (US)
Pages (from-to)48-69
Number of pages22
JournalClinical Chemistry
Volume62
Issue number1
DOIs
StatePublished - Jan 1 2016

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Mass spectrometry
Assays
Mass Spectrometry
Peptides
Proteins
Clinical laboratories
Proteolysis
National Cancer Institute (U.S.)
Workflow
Drug Industry
Proteomics
Transparency
Tumors
Industry
Research Personnel
Amino Acids
Sensitivity and Specificity
Research
Pharmaceutical Preparations
Neoplasms

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical

Cite this

Hoofnagle, A. N., Whiteaker, J. R., Carr, S. A., Kuhn, E., Liu, T., Massoni, S. A., ... Paulovich, A. G. (2016). Recommendations for the generation, quantification, storage, and handling of peptides used for mass spectrometry-based assays. Clinical Chemistry, 62(1), 48-69. https://doi.org/10.1373/clinchem.2015.250563

Recommendations for the generation, quantification, storage, and handling of peptides used for mass spectrometry-based assays. / Hoofnagle, Andrew N.; Whiteaker, Jeffrey R.; Carr, Steven A.; Kuhn, Eric; Liu, Tao; Massoni, Sam A.; Thomas, Stefani N.; Reid Townsend, R.; Zimmerman, Lisa J.; Boja, Emily; Chen, Jing; Crimmins, Daniel L.; Davies, Sherri R.; Gao, Yuqian; Hiltke, Tara R.; Ketchum, Karen A.; Kinsinger, Christopher R.; Mesri, Mehdi; Meyer, Matthew R.; Qian, Wei Jun; Schoenherr, Regine M.; Scott, Mitchell G.; Shi, Tujin; Whiteley, Gordon R.; Wrobel, John A.; Wu, Chaochao; Ackermann, Brad L.; Aebersold, Ruedi; Barnidge, David R.; Bunk, David M.; Clarke, Nigel; Fishman, Jordan B.; Grant, Russ P.; Kusebauch, Ulrike; Kushnir, Mark M.; Lowenthal, Mark S.; Moritz, Robert L.; Neubert, Hendrik; Patterson, Scott D.; Rockwood, Alan L.; Rogers, John; Singh, Ravinder J.; Van Eyk, Jennifer E.; Wong, Steven H.; Zhang, Shucha; Chan, Daniel Wan-Yui; Chen, Xian; Ellis, Matthew J.; Liebler, Daniel C.; Rodland, Karin D.; Rodriguez, Henry; Smith, Richard D.; Zhang, Zhen; Zhang, Hui; Paulovich, Amanda G.

In: Clinical Chemistry, Vol. 62, No. 1, 01.01.2016, p. 48-69.

Research output: Contribution to journalArticle

Hoofnagle, AN, Whiteaker, JR, Carr, SA, Kuhn, E, Liu, T, Massoni, SA, Thomas, SN, Reid Townsend, R, Zimmerman, LJ, Boja, E, Chen, J, Crimmins, DL, Davies, SR, Gao, Y, Hiltke, TR, Ketchum, KA, Kinsinger, CR, Mesri, M, Meyer, MR, Qian, WJ, Schoenherr, RM, Scott, MG, Shi, T, Whiteley, GR, Wrobel, JA, Wu, C, Ackermann, BL, Aebersold, R, Barnidge, DR, Bunk, DM, Clarke, N, Fishman, JB, Grant, RP, Kusebauch, U, Kushnir, MM, Lowenthal, MS, Moritz, RL, Neubert, H, Patterson, SD, Rockwood, AL, Rogers, J, Singh, RJ, Van Eyk, JE, Wong, SH, Zhang, S, Chan, DW-Y, Chen, X, Ellis, MJ, Liebler, DC, Rodland, KD, Rodriguez, H, Smith, RD, Zhang, Z, Zhang, H & Paulovich, AG 2016, 'Recommendations for the generation, quantification, storage, and handling of peptides used for mass spectrometry-based assays', Clinical Chemistry, vol. 62, no. 1, pp. 48-69. https://doi.org/10.1373/clinchem.2015.250563
Hoofnagle, Andrew N. ; Whiteaker, Jeffrey R. ; Carr, Steven A. ; Kuhn, Eric ; Liu, Tao ; Massoni, Sam A. ; Thomas, Stefani N. ; Reid Townsend, R. ; Zimmerman, Lisa J. ; Boja, Emily ; Chen, Jing ; Crimmins, Daniel L. ; Davies, Sherri R. ; Gao, Yuqian ; Hiltke, Tara R. ; Ketchum, Karen A. ; Kinsinger, Christopher R. ; Mesri, Mehdi ; Meyer, Matthew R. ; Qian, Wei Jun ; Schoenherr, Regine M. ; Scott, Mitchell G. ; Shi, Tujin ; Whiteley, Gordon R. ; Wrobel, John A. ; Wu, Chaochao ; Ackermann, Brad L. ; Aebersold, Ruedi ; Barnidge, David R. ; Bunk, David M. ; Clarke, Nigel ; Fishman, Jordan B. ; Grant, Russ P. ; Kusebauch, Ulrike ; Kushnir, Mark M. ; Lowenthal, Mark S. ; Moritz, Robert L. ; Neubert, Hendrik ; Patterson, Scott D. ; Rockwood, Alan L. ; Rogers, John ; Singh, Ravinder J. ; Van Eyk, Jennifer E. ; Wong, Steven H. ; Zhang, Shucha ; Chan, Daniel Wan-Yui ; Chen, Xian ; Ellis, Matthew J. ; Liebler, Daniel C. ; Rodland, Karin D. ; Rodriguez, Henry ; Smith, Richard D. ; Zhang, Zhen ; Zhang, Hui ; Paulovich, Amanda G. / Recommendations for the generation, quantification, storage, and handling of peptides used for mass spectrometry-based assays. In: Clinical Chemistry. 2016 ; Vol. 62, No. 1. pp. 48-69.
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AU - Hoofnagle, Andrew N.

AU - Whiteaker, Jeffrey R.

AU - Carr, Steven A.

AU - Kuhn, Eric

AU - Liu, Tao

AU - Massoni, Sam A.

AU - Thomas, Stefani N.

AU - Reid Townsend, R.

AU - Zimmerman, Lisa J.

AU - Boja, Emily

AU - Chen, Jing

AU - Crimmins, Daniel L.

AU - Davies, Sherri R.

AU - Gao, Yuqian

AU - Hiltke, Tara R.

AU - Ketchum, Karen A.

AU - Kinsinger, Christopher R.

AU - Mesri, Mehdi

AU - Meyer, Matthew R.

AU - Qian, Wei Jun

AU - Schoenherr, Regine M.

AU - Scott, Mitchell G.

AU - Shi, Tujin

AU - Whiteley, Gordon R.

AU - Wrobel, John A.

AU - Wu, Chaochao

AU - Ackermann, Brad L.

AU - Aebersold, Ruedi

AU - Barnidge, David R.

AU - Bunk, David M.

AU - Clarke, Nigel

AU - Fishman, Jordan B.

AU - Grant, Russ P.

AU - Kusebauch, Ulrike

AU - Kushnir, Mark M.

AU - Lowenthal, Mark S.

AU - Moritz, Robert L.

AU - Neubert, Hendrik

AU - Patterson, Scott D.

AU - Rockwood, Alan L.

AU - Rogers, John

AU - Singh, Ravinder J.

AU - Van Eyk, Jennifer E.

AU - Wong, Steven H.

AU - Zhang, Shucha

AU - Chan, Daniel Wan-Yui

AU - Chen, Xian

AU - Ellis, Matthew J.

AU - Liebler, Daniel C.

AU - Rodland, Karin D.

AU - Rodriguez, Henry

AU - Smith, Richard D.

AU - Zhang, Zhen

AU - Zhang, Hui

AU - Paulovich, Amanda G.

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