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 QianRegine 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 W. Chan, Xian Chen, Matthew J. Ellis, Daniel C. Liebler, Karin D. Rodland, Henry Rodriguez, Richard D. Smith, Zhen Zhang, Hui Zhang, Amanda G. Paulovich

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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 2016
Externally publishedYes

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Hoofnagle, A. N., Whiteaker, J. R., Carr, S. A., Kuhn, E., Liu, T., Massoni, S. A., Thomas, S. N., Reid Townsend, R., Zimmerman, L. J., Boja, E., Chen, J., Crimmins, D. L., Davies, S. R., Gao, Y., Hiltke, T. R., Ketchum, K. A., Kinsinger, C. R., Mesri, M., Meyer, M. R., ... 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