Revisiting biomarker discovery by plasma proteomics

被引：622

作者：

Geyer, Philipp E. ^{[1
,2
]}

Holdt, Lesca M. ^{[3
]}

Teupser, Daniel ^{[3
]}

Mann, Matthias ^{[1
,2
]}

机构：

[1] Max Planck Inst Biochem, Dept Prote & Signal Transduct, Martinsried, Germany

[2] Univ Copenhagen, NNF Ctr Prot Res, Fac Hlth Sci, Copenhagen, Denmark

[3] Univ Hosp, LMU Munich, Inst Lab Med, Munich, Germany

来源：

MOLECULAR SYSTEMS BIOLOGY | 2017年 / 13卷 / 09期

关键词：

biomarkers; diagnostic; mass spectrometry; plasma proteomics; systems medicine; MASS-SPECTROMETRY; TARGETED PROTEOMICS; ABUNDANCE PROTEINS; CANCER BIOMARKERS; QUANTIFICATION; SERUM; VALIDATION; PEPTIDE; IDENTIFICATION; VERIFICATION;

D O I：

10.15252/msb.20156297

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Clinical analysis of blood is the most widespread diagnostic procedure in medicine, and blood biomarkers are used to categorize patients and to support treatment decisions. However, existing biomarkers are far from comprehensive and often lack specificity and new ones are being developed at a very slow rate. As described in this review, mass spectrometry (MS)-based proteomics has become a powerful technology in biological research and it is now poised to allow the characterization of the plasma proteome in great depth. Previous "triangular strategies" aimed at discovering single biomarker candidates in small cohorts, followed by classical immunoassays in much larger validation cohorts. We propose a "rectangular" plasma proteome profiling strategy, in which the proteome patterns of large cohorts are correlated with their phenotypes in health and disease. Translating such concepts into clinical practice will require restructuring several aspects of diagnostic decision-making, and we discuss some first steps in this direction.

引用

页数：15

共 96 条

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

Abbatiello, Susan E. ;

Schilling, Birgit ;

Mani, D. R. ;

Zimmerman, Lisa J. ;

Hall, Steven C. ;

Maclean, Brendan ;

Albertolle, Matthew ;

Allen, Simon ;

Burgess, Michael ;

Cusack, Michael P. ;

Gosh, Mousumi ;

Hedrick, Victoria ;

Held, Jason M. ;

Inerowicz, H. Dorota ;

Jackson, Angela ;

Keshishian, Hasmik ;

Kinsinger, Christopher R. ;

Lyssand, John ;

Makowski, Lee ;

Mesri, Mehdi ;

Rodriguez, Henry ;

Rudnick, Paul ;

Sadowski, Pawel ;

Sedransk, Nell ;

Shaddox, Kent ;

Skates, Stephen J. ;

Kuhn, Eric ;

Smith, Derek ;

Whiteaker, Jeffery R. ;

Whitwell, Corbin ;

Zhang, Shucha ;

Borchers, Christoph H. ;

Fisher, Susan J. ;

Gibson, Bradford W. ;

Liebler, Daniel C. ;

MacCoss, Michael J. ;

Neubert, Thomas A. ;

Paulovich, Amanda G. ;

Regnier, Fred E. ;

Tempst, Paul ;

Carr, Steven A. .

MOLECULAR & CELLULAR PROTEOMICS, 2015, 14 (09) :2357-2374

[2] 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

[3] Mass-spectrometric exploration of proteome structure and function [J].

Aebersold, Ruedi ;

Mann, Matthias .

NATURE, 2016, 537 (7620) :347-355

[4] Trends in ultrasensitive proteomics [J].

Altelaar, A. F. Maarten ;

Heck, Albert J. R. .

CURRENT OPINION IN CHEMICAL BIOLOGY, 2012, 16 (1-2) :206-213

[5] The Riddle of Protein Diagnostics: Future Bleak or Bright? [J].

Anderson, N. Leigh ;

Ptolemy, Adam S. ;

Rifai, Nader .

CLINICAL CHEMISTRY, 2013, 59 (01) :194-197

[6] The Clinical Plasma Proteome: A Survey of Clinical Assays for Proteins in Plasma and Serum [J].

Anderson, N. Leigh .

CLINICAL CHEMISTRY, 2010, 56 (02) :177-185

[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] Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments [J].

Baggerly, KA ;

Morris, JS ;

Coombes, KR .

BIOINFORMATICS, 2004, 20 (05) :777-U710

[9] Robust and sensitive iTRAQ quantification on an LTQ orbitrap mass spectrometer [J].

Bantscheff, Marcus ;

Boesche, Markus ;

Eberhard, Dirk ;

Matthieson, Toby ;

Sweetman, Gavain ;

Kuster, Bernhard .

MOLECULAR & CELLULAR PROTEOMICS, 2008, 7 (09) :1702-1713

[10] An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes [J].

Bekker-Jensen, Dorte B. ;

Kelstrup, Christian D. ;

Batth, Tanveer S. ;

Larsen, Sara C. ;

Haldrup, Christa ;

Bramsen, Jesper B. ;

Sorensen, Karina D. ;

Hoyer, Soren ;

Orntoft, Torben F. ;

Andersen, Claus L. ;

Nielsen, Michael L. ;

Olsen, Jesper V. .

CELL SYSTEMS, 2017, 4 (06) :587-+

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