Moving towards high density clinical signature studies with a human proteome catalogue developing multiplexing mass spectrometry assay panels
Open accessAbstract
A perspective overview is given describing the current development of multiplex mass spectrometry assay technology platforms utilized for high throughput clinical sample analysis. The development of targeted therapies with novel personalized medicine drugs will require new tools for monitoring efficacy and outcome that will rely on both the quantification of disease progression related biomarkers as well as the measurement of disease specific pathway/signaling proteins.The bioinformatics developments play a key central role in the area of clinical proteomics where targeted peptide expressions in health and disease are investigated in small-, medium- and large-scaled clinical studies.An outline is presented describing applications of the selected reaction monitoring (SRM) mass spectrometry assay principle. This assay form enables the simultaneous description of multiple protein biomarkers and is an area under a fast and progressive development throughout the community. The Human Proteome Organization, HUPO, recently launched the Human Proteome Project (HPP) that will map the organization of proteins on specific chromosomes, on a chromosome-by-chromosome basis utilizing the SRM technology platform. Specific examples of an SRM-multiplex quantitative assay platform dedicated to the cardiovascular disease area, screening Apo A1, Apo A4, Apo B, Apo CI, Apo CII, Apo CIII, Apo D, Apo E, Apo H, and CRP biomarkers used in daily diagnosis routines in clinical hospitals globally, are presented. We also provide data on prostate cancer studies that have identified a variety of PSA isoforms characterized by high-resolution separation interfaced to mass spectrometry.
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Various LC-MS/MS assays for multiplexed quantification of apolipoproteins or phenotyping of apoE have been reported.
“Various LC-MS/MS assays for multiplexed quantification of apolipoproteins (14-23) or phenotyping of apoE (24-27) have been reported.”
From Automated multiplex LC-MS/MS assay for quantifying serum apolipoproteins A-I, B, C-I, C-II, C-III, and E with qualitative apolipoprotein E phenotyping (2016) · cites this paper as [17]
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Cites
Systems Biology and New Technologies Enable Predictive and Preventative Medicine
Hood, L., Heath, J. R., Phelps, M. E., & Lin, B. (2004) · Science · doi:10.1126/science.1104635 · Cited by 1,108 · cited 1× · see citing works
“This change in modern hospital infrastructure has already started, and is to a large extent a technology driven research commodity [1].”
BackgroundOn the Development of Plasma Protein Biomarkers
Surinova, S., Schiess, R., Hüttenhain, R., Cerciello, F., Wollscheid, B., & Aebersold, R. (2011) · Journal of Proteome Research · doi:10.1021/pr1008515 · Cited by 334 · cited 1× · see citing works
“Today, the multiplex SRM sensitivity limitation of a given protein is in the low ng/mL [27,29].”
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Research works printed but not linked: 38
- Marko-Varga G Lindberg H Lofdahl CG Jonsson P Hansson L Dahlback M Lindquist E Johansson L Foster M Fehniger TE Discovery of biomarker candidates within disease by protein profiling: Principles and concepts J Proteome Res 2005 4 1200 1212 10.1021/pr050122w 16083270 · DOI
- Taylor CF Paton NW Lilley KS Binz PA Julian RK Jones AR Zhu WM Apweiler R Aebersold R Deutsch EW The minimum information about a proteomics experiment (MIAPE) Nat Biotechnol 2007 25 887 893 10.1038/nbt1329 17687369 · DOI
- Taylor CE Minimum reporting requirements for proteomics: A MIAPE primer Proteomics 2006 39 44 10.1002/pmic.200600549 17031795 · DOI
- Wright JC Hubbard SJ Recent Developments in Proteome Informatics for Mass Spectrometry Analysis Comb Chem High T Scr 2009 12 194 202 19199887
- Orchard S Jones A Albar JP Cho SY Kwon KH Lee C Hermjakob H Tackling Quantitation: A Report on the Annual Spring Workshop of the HUPO-PSI Proteomics 2010 10 3062 3066 10.1002/pmic.201090075 20806224 · DOI
- Baker MS Building the 'practical' human proteome project - The next big thing in basic and clinical proteomics Curr Opin Mol Ther 2009 11 600 602 20077630
- Hochstrasser D Should the Human Proteome Project Be Gene- or Protein-centric? J Proteome Res 2008 7 5071 5071 10.1021/pr800884r 19367715 · DOI
- A Gene-centric Human Proteome Project Mol Cell Prot 2010 9 427 429 10.1074/mcp.H900001-MCP200 PMC2830851 20124355 · DOI
- Atkinson AJ Colburn WA DeGruttola VG DeMets DL Downing GJ Hoth DF Oates JA Peck CC Schooley RT Spilker BA Biomarkers and surrogate endpoints: Preferred definitions and conceptual framework* Clin Pharmacol Ther 2001 69 89 95 10.1067/mcp.2001.113989 11240971 · DOI
- Marko-Varga G Ogiwara A Nishimura T Kawamura T Fujii K Kawakami T Kyono Y Tu HK Anyoji H Kanazawa M Personalized medicine and proteomics: Lessons from non-small cell lung cancer J Proteome Res 2007 6 2925 2935 10.1021/pr070046s 17636986 · DOI
- Lander ES Linton LM Birren B Nusbaum C Zody MC Baldwin J Devon K Dewar K Doyle M FitzHugh W Initial sequencing and analysis of the human genome Nature 2001 409 860 921 10.1038/35057062 11237011 · DOI · Paper page
- Venter JC Adams MD Myers EW Li PW Mural RJ Sutton GG Smith HO Yandell M Evans CA Holt RA The sequence of the human genome Science 2001 291 1304 1351 10.1126/science.1058040 11181995 · DOI · Paper page
- Collins FS Morgan M Patrinos A The human genome project: Lessons from large-scale biology Science 2003 300 286 290 10.1126/science.1084564 12690187 · DOI · Paper page
- Jasny BR Roberts L Unlocking the genome Science 2001 294 81 81 10.1126/science.294.5540.81 11588244 · DOI
- Hancock W Omenn G LeGrain P Paik YK Proteomics, Human Proteome Project, and Chromosomes J Proteome Res 2011 10 210 210 10.1021/pr101099h 21114295 · DOI
- Aebersold R Auffray C Baney E Barillot E Brazma A Brett C Brunak S Butte A Califano A Celis J Report on EU-USA Workshop: How Systems Biology Can Advance Cancer Research (27 October 2008) Mol Oncol 2009 3 9 17 10.1016/j.molonc.2008.11.003 19383362 PMC2930781 · DOI
- Fehniger TE Marko-Varga G Clinical Proteomics Today J Proteome Res 2011 10 3 3 10.1021/pr1012569 21210716 · DOI
- Hood L A Personal Journey of Discovery: Developing Technology and Changing Biology Annu Rev Anal Chem 2008 1 1 43 10.1146/annurev.anchem.1.031207.113113 20636073 · DOI
- Anderson NL The Clinical Plasma Proteome: A Survey of Clinical Assays for Proteins in Plasma and Serum Clin Chem 2010 56 177 185 10.1373/clinchem.2009.126706 19884488 · DOI
- Anderson L Hunter CL Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins Mol Cell Prot 2006 5 573 588 10.1074/mcp.M500331-MCP200 16332733 · DOI · Paper page
- Hu Z Hood L Tan O Quantitative proteomic approaches for biomarker discovery Proteom Clin Appl 2007 1 1036 1041 10.1002/prca.200700109 21136755 · DOI
- Weston AD Hood L Systems biology, proteomics, and the future of health care: Toward predictive, preventative, and personalized medicine J Proteome Res 2004 3 179 196 10.1021/pr0499693 15113093 · DOI
- Lange V Picotti P Domon B Aebersold R Selected reaction monitoring for quantitative proteomics: a tutorial Mol Sys Biol 2008 4 Article number: 222 PMC2583086 18854821
- Hüttenhain R Malmström J Picotti P Aebersold R Perspectives of targeted mass spectrometry for protein biomarker verification Curr Opin Chem Biol 2009 13 518 525 19818677 PMC2795387
- Abbatiello SE Mani DR Keshishian H Carr SA Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry Clin Chem 2010 56 291 305 10.1373/clinchem.2009.138420 20022980 PMC2851178 · DOI
- Ong SE Schenone M Margolin AA Li XY Do K Doud MK Mani DR Kuai L Wang X Wood JL Identifying the proteins to which small-molecule probes and drugs bind in cells Proc Natl Acad Sci USA 2009 106 4617 4622 10.1073/pnas.0900191106 19255428 PMC2649954 · DOI
- Finnskog D Järås K Ressine A Malm J Marko-Varga G Lilja H Laurell T High-speed biomarker identification utilizing porous silicon nanovial arrays and MALDI-TOF mass spectrometry Electrophoresis 2006 27 1093 1103 10.1002/elps.200500751 16523454 · DOI
- Klein RJ Hallden C Cronin AM Ploner A Wiklund F Bjartell AS Stattin P Xu JF Scardino PT Offit K Blood Biomarker Levels to Aid Discovery of Cancer-Related Single-Nucleotide Polymorphisms: Kallikreins and Prostate Cancer Cancer Prev Res 2010 3 611 619 10.1158/1940-6207.CAPR-09-0206 PMC2865570 20424135 · DOI
- Steuber T Vickers AJ Serio AM Vaisanen V Haese A Pettersson K Eastham JA Scardino PT Huland H Lilja H Comparison of free and total forms of serum human kallikrein 2 and prostate-specific antigen for prediction of locally advanced and recurrent prostate cancer Clin Chem 2007 53 233 240 10.1373/clinchem.2006.074963 17185368 · DOI
- Vickers AJ Cronin AM Roobol MJ Savage CJ Peltola M Pettersson K Scardino PT Schroder FH Lilja H A Four-Kallikrein Panel Predicts Prostate Cancer in Men with Recent Screening: Data from the European Randomized Study of Screening for Prostate Cancer, Rotterdam Clin Chem Res 2010 16 3232 3239 10.1158/1078-0432.CCR-10-0122 PMC2891337 20400522 · DOI
- Végvári Á Rezeli M Welinder C Malm J Lilja H Marko-Varga G Laurell T Identification of Prostate Specific Antigen (PSA) Isoforms in Complex Biological Samples Utilizing Complementary Platforms J Proteomics 2010 73 1137 1147 20102753 PMC2856840
- Végvári Á Rezeli M Sihlbom C Carlsohn E Malm J Lilja H Laurell T Marko-Varga G Marko-Varga G, Simones T Characterization of PSA in Clinical Samples by Mass Spectrometry 4th EuPA Scientific Meeting - A Proteomics Odyssey Towards Next Decades; Estoril, Portugal 2010 Ook-Press Ltd 508 510
- Végvári Á Marko-Varga G Clinical Protein Science and Bioanalytical Mass Spectrometry with an Emphasis on Lung Cancer Chem Rev 2010 110 3278 3298 20415473
- Choudhary C Mann M Decoding signalling networks by mass spectrometry-based proteomics Nat Rev Mol Cell Biol 2010 11 427 439 10.1038/nrm2900 20461098 · DOI
- Kiyonami R Domon B Selected reaction monitoring applied to quantitative proteomics Methods Mol Biol 2010 658 155 166 full_text 20839103
- Picotti P Rinner O Stallmach R Dautel F Farrah T Domon B Wenschuh H Aebersold R High-throughput generation of selected reaction-monitoring assays for proteins and proteomes Nat Methods 2010 7 43 U45 10.1038/nmeth.1408 19966807 · DOI
- Zhan XQ Desiderio DM The human pituitary nitroproteome: detection of nitrotyrosyl-proteins with two-dimensional Western blotting, and amino acid sequence determination with mass spectrometry Biochem Biophys Res Commun 2004 325 1180 1186 10.1016/j.bbrc.2004.10.169 15555551 · DOI
- Zhan XQ Desiderio DM The use of variations in proteomes to predict, prevent, and personalize treatment for clinically nonfunctional pituitary adenomas The EPMA Journal 2010 1 439 459 10.1007/s13167-010-0028-z PMC3405333 23199087 · DOI
Cited by
Sorted by citations
van den Broek, I., Romijn, F. P. H. T. M., Nouta, J., van der Laarse, A., Drijfhout, J. W., Smit, N. P. M., van der Burgt, Y. E. M., & Cobbaert, C. M. (2016) · Clinical Chemistry · doi:10.1373/clinchem.2015.246702 · Cited by 105 · see citing works
- Authors
- Rezeli, M., Végvári, Á., Fehniger, T. E., Laurell, T., & Marko-Varga, G.
- Affiliations
- Lund University (SE)
- Tallinn University of Technology (EE)
- Venue
- Journal of Clinical Bioinformatics
- Publisher
- ClinTransMed, AB
- Published
- 2011
- Volume
- 1
- Issue
- 1
- Pages
- 7
- ISSN
- 2043-9113 (ISSN-L)
- PMC
- PMC3164614
- OpenAlex
- W2103909204
- Cited by
- 15
- References
- 2
- Citations by year
- 2020: 1 · 2018: 1 · 2017: 3 · 2015: 2 · 2014: 2 · 2013: 4 · 2012: 1
- FWCI
- 1.16
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Journal of Clinical Bioinformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Lund University Publications (Lund University) (submittedVersion, other-oa)
- Funders
- Cancerfonden
- Knut och Alice Wallenbergs Stiftelse
- Vetenskapsrådet (20095)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- multiple reaction monitoring, targeted proteomics, clinical proteomics, Human Proteome Project, cardiovascular biomarkers, C-reactive protein, prostate cancer, PSA isoforms, personalized medicine, biomarker quantification
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