Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma

被引：142

作者：

Abbatiello, Susan E. ^{[1
]}

Schilling, Birgit ^{[2
]}

Mani, D. R. ^{[1
]}

Zimmerman, Lisa J. ^{[3
,4
]}

Hall, Steven C. ^{[5
]}

Maclean, Brendan ^{[6
]}

Albertolle, Matthew ^{[5
]}

Allen, Simon ^{[5
]}

Burgess, Michael ^{[1
]}

Cusack, Michael P. ^{[2
]}

Gosh, Mousumi ^{[7
]}

Hedrick, Victoria ^{[8
]}

Held, Jason M. ^{[2
]}

Inerowicz, H. Dorota ^{[8
]}

Jackson, Angela ^{[9
]}

Keshishian, Hasmik ^{[1
]}

Kinsinger, Christopher R. ^{[10
]}

Lyssand, John ^{[11
]}

Makowski, Lee

Mesri, Mehdi ^{[10
]}

Rodriguez, Henry ^{[10
]}

Rudnick, Paul ^{[12
]}

Sadowski, Pawel ^{[11
]}

Sedransk, Nell ^{[13
]}

Shaddox, Kent ^{[3
,4
]}

Skates, Stephen J. ^{[14
]}

Kuhn, Eric ^{[1
]}

Smith, Derek ^{[9
]}

Whiteaker, Jeffery R. ^{[15
]}

Whitwell, Corbin ^{[3
,4
]}

Zhang, Shucha ^{[15
]}

Borchers, Christoph H. ^{[9
]}

Fisher, Susan J. ^{[5
]}

Gibson, Bradford W. ^{[2
]}

Liebler, Daniel C. ^{[3
,4
]}

MacCoss, Michael J. ^{[6
]}

Neubert, Thomas A. ^{[10
,11
]}

Paulovich, Amanda G. ^{[15
]}

Regnier, Fred E. ^{[8
]}

Tempst, Paul ^{[7
]}

Carr, Steven A. ^{[1
]}

机构：

[1] Broad Inst & Harvard, Cambridge, MA 02142 USA

[2] Buck Inst Res Aging, Novato, CA 94945 USA

[3] Vanderbilt Univ, Sch Med, Dept Biochem, Nashville, TN 37232 USA

[4] Vanderbilt Ingram Canc Ctr, Jim Ayers Inst Precancer Detect & Diag, Nashville, TN 37232 USA

[5] Univ Calif San Francisco, Dept Obstet Gynecol & Reprod Sci, San Francisco, CA 94143 USA

[6] Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA USA

[7] Mem Sloan Kettering Canc Ctr, New York, NY 10065 USA

[8] Purdue Univ, W Lafayette, IN 47907 USA

[9] Univ Victoria, Genome BC Prote Ctr, Victoria, BC V8Z 7X8, Canada

[10] NCI, NIH, Bethesda, MD 20892 USA

[11] NYU, Skirball Inst, Kimmel Ctr Biol & Med, New York, NY 10016 USA

[12] NIST, Gaithersburg, MD 20899 USA

[13] Natl Inst Stat Sci, Res Triangle Pk, NC 27709 USA

[14] Massachusetts Gen Hosp, Biostat Ctr, Boston, MA 02114 USA

[15] Fred Hutchinson Canc Res Ctr, Seattle, WA 98109 USA

来源：

MOLECULAR & CELLULAR PROTEOMICS | 2015年 / 14卷 / 09期

关键词：

SPECTROMETRY-BASED QUANTIFICATION; MONITORING MASS-SPECTROMETRY; LOW-ABUNDANCE PROTEINS; ABSOLUTE QUANTIFICATION; BIOMARKER DISCOVERY; TARGETED PROTEOMICS; STANDARDS; PROTEOLYSIS; PERFORMANCE; PROTOCOL;

D O I：

10.1074/mcp.M114.047050

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens to hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility, and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here, we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and seven control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data, we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to sub-nanogram/ml sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and interlaboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy-isotope-labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an interlaboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality control measures, enables sensitive, specific, reproducible, and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.

引用

页码：2357 / 2374

页数：18

共 59 条

[1] Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (LC-MRM-MS) [J].

Abbatiello, Susan E. ;

Mani, D. R. ;

Schilling, Birgit ;

MacLean, Brendan ;

Zimmerman, Lisa J. ;

Feng, Xingdong ;

Cusack, Michael P. ;

Sedransk, Nell ;

Hall, Steven C. ;

Addona, Terri ;

Allen, Simon ;

Dodder, Nathan G. ;

Ghosh, Mousumi ;

Held, Jason M. ;

Hedrick, Victoria ;

Inerowicz, H. Dorota ;

Jackson, Angela ;

Keshishian, Hasmik ;

Kim, Jong Won ;

Lyssand, John S. ;

Riley, C. Paige ;

Rudnick, Paul ;

Sadowski, Pawel ;

Shaddox, Kent ;

Smith, Derek ;

Tomazela, Daniela ;

Wahlander, Asa ;

Waldemarson, Sofia ;

Whitwell, Corbin A. ;

You, Jinsam ;

Zhang, Shucha ;

Kinsinger, Christopher R. ;

Mesri, Mehdi ;

Rodriguez, Henry ;

Borchers, Christoph H. ;

Buck, Charles ;

Fisher, Susan J. ;

Gibson, Bradford W. ;

Liebler, Daniel ;

MacCoss, Michael ;

Neubert, Thomas A. ;

Paulovich, Amanda ;

Regnier, Fred ;

Skates, Steven J. ;

Tempst, Paul ;

Wang, Mu ;

Carr, Steven A. .

MOLECULAR & CELLULAR PROTEOMICS, 2013, 12 (09) :2623-2639

[2] Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry [J].

Abbatiello, Susan E. ;

Mani, D. R. ;

Keshishian, Hasmik ;

Carr, Steven A. .

CLINICAL CHEMISTRY, 2010, 56 (02) :291-305

[3] A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease [J].

Addona, Terri A. ;

Shi, Xu ;

Keshishian, Hasmik ;

Mani, D. R. ;

Burgess, Michael ;

Gillette, Michael A. ;

Clauser, Karl R. ;

Shen, Dongxiao ;

Lewis, Gregory D. ;

Farrell, Laurie A. ;

Fifer, Michael A. ;

Sabatine, Marc S. ;

Gerszten, Robert E. ;

Carr, Steven A. .

NATURE BIOTECHNOLOGY, 2011, 29 (07) :635-U119

[4] Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma [J].

Addona, Terri A. ;

Abbatiello, Susan E. ;

Schilling, Birgit ;

Skates, Steven J. ;

Mani, D. R. ;

Bunk, David M. ;

Spiegelman, Clifford H. ;

Zimmerman, Lisa J. ;

Ham, Amy-Joan L. ;

Keshishian, Hasmik ;

Hall, Steven C. ;

Allen, Simon ;

Blackman, Ronald K. ;

Borchers, Christoph H. ;

Buck, Charles ;

Cardasis, Helene L. ;

Cusack, Michael P. ;

Dodder, Nathan G. ;

Gibson, Bradford W. ;

Held, Jason M. ;

Hiltke, Tara ;

Jackson, Angela ;

Johansen, Eric B. ;

Kinsinger, Christopher R. ;

Li, Jing ;

Mesri, Mehdi ;

Neubert, Thomas A. ;

Niles, Richard K. ;

Pulsipher, Trenton C. ;

Ransohoff, David ;

Rodriguez, Henry ;

Rudnick, Paul A. ;

Smith, Derek ;

Tabb, David L. ;

Tegeler, Tony J. ;

Variyath, Asokan M. ;

Vega-Montoto, Lorenzo J. ;

Wahlander, Asa ;

Waldemarson, Sofia ;

Wang, Mu ;

Whiteaker, Jeffrey R. ;

Zhao, Lei ;

Anderson, N. Leigh ;

Fisher, Susan J. ;

Liebler, Daniel C. ;

Paulovich, Amanda G. ;

Regnier, Fred E. ;

Tempst, Paul ;

Carr, Steven A. .

NATURE BIOTECHNOLOGY, 2009, 27 (07) :633-U85

[5] Simultaneous Quantification of Apolipoprotein A-I and Apolipoprotein B by Liquid-Chromatography-Multiple-Reaction-Monitoring Mass Spectrometry [J].

Agger, Sean A. ;

Marney, Luke C. ;

Hoofnagle, Andrew N. .

CLINICAL CHEMISTRY, 2010, 56 (12) :1804-1813

[6] Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins [J].

Anderson, L ;

Hunter, CL .

MOLECULAR & CELLULAR PROTEOMICS, 2006, 5 (04) :573-588

[7] Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide antibodies (SISCAPA) [J].

Anderson, NL ;

Anderson, NG ;

Haines, LR ;

Hardie, DB ;

Olafson, RW ;

Pearson, TW .

JOURNAL OF PROTEOME RESEARCH, 2004, 3 (02) :235-244

[8]

[Anonymous], P 59 ANN ASMS C MASS

[9]

[Anonymous], CURRENT PROTOCOLS BI

[10]

Armbruster David A, 2008, Clin Biochem Rev, V29 Suppl 1, pS49

← 1 2 3 4 5 6 →