Mass spectrometry-based proteomic quest for diabetes biomarkers

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1854, Issue 6, 2015, Pages 519-527

  Shao, Shiying ^a,b   Guo, Tiannan ^b   Aebersold, Ruedi ^b,c  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b ETH ZURICH   (Switzerland)

^c UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Biomarker; Diabetes; Mass spectrometry; Proteomics; Selected reaction monitoring; SWATH MS

Indexed keywords

BIOLOGICAL MARKER;

ANIMAL; DIABETES MELLITUS; HUMAN; MASS SPECTROMETRY; METABOLISM; PROCEDURES; PROTEOMICS;

ANIMALS; BIOLOGICAL MARKERS; BIOMARKERS; DIABETES MELLITUS; HUMANS; MASS SPECTROMETRY; PROTEOMICS;

EID: 84939961434     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2014.12.012     Document Type: Review

References (73)

1. J.E. Shaw, R.A. Sicree, and P.Z. Zimmet Global estimates of the prevalence of diabetes for 2010 and 2030 Diabetes Res. Clin. Pract. 87 2010 4 14
2. K.G. Alberti, and P.Z. Zimmet Definition, diagnosis and classification of diabetes mellitus and its complications. Part 1: diagnosis and classification of diabetes mellitus provisional report of a WHO consultation Diabet. Med. 15 1998 539 553
3. Type 1 diabetes - progress and prospects Lancet 383 2014 2
4. R.P. Robertson, J. Harmon, P.O. Tran, and V. Poitout Beta-cell glucose toxicity, lipotoxicity, and chronic oxidative stress in type 2 diabetes Diabetes 53 Suppl. 1 2004 S119 S124
5. S. Shao, Y. Yang, G. Yuan, M. Zhang, and X. Yu Signaling molecules involved in lipid-induced pancreatic beta-cell dysfunction DNA Cell Biol. 32 2013 41 49
6. A. American diabetes, diagnosis and classification of diabetes mellitus Diabetes Care 36 Suppl. 1 2013 S67 S74
7. D.M. Nathan Long-term complications of diabetes mellitus N. Engl. J. Med. 328 1993 1676 1685
8. T. Kuzuya, S. Nakagawa, J. Satoh, Y. Kanazawa, Y. Iwamoto, M. Kobayashi, K. Nanjo, A. Sasaki, Y. Seino, C. Ito, K. Shima, K. Nonaka, and T. Kadowaki Committee of the Japan Diabetes Society on thediagnostic criteria of diabetes mellitus, Report of the Committee on the classification and diagnostic criteria of diabetes mellitus Diabetes Res. Clin. Pract. 55 2002 65 85
9. R.G. Barr, D.M. Nathan, J.B. Meigs, and D.E. Singer Tests of glycemia for the diagnosis of type 2 diabetes mellitus Ann. Intern. Med. 137 2002 263 272
10. H. Glauber, and E. Karnieli Preventing type 2 diabetes mellitus: a call for personalized intervention Perm. J. 17 2013 74 79
11. Y. Heianza, Y. Arase, K. Fujihara, H. Tsuji, K. Saito, S.D. Hsieh, S. Kodama, H. Shimano, N. Yamada, S. Hara, and H. Sone Screening for pre-diabetes to predict future diabetes using various cut-off points for HbA(1c) and impaired fasting glucose: the Toranomon Hospital Health Management Center Study 4 (TOPICS 4) Diabet. Med. 29 2012 e279 e285
12. M. Knip, R. Veijola, S.M. Virtanen, H. Hyoty, O. Vaarala, and H.K. Akerblom Environmental triggers and determinants of type 1 diabetes Diabetes 54 Suppl. 2 2005 S125 S136
13. J.M. Barker, K.J. Barriga, L. Yu, D. Miao, H.A. Erlich, J.M. Norris, G.S. Eisenbarth, and M. Rewers Diabetes autoimmunity study in the, prediction of autoantibody positivity and progression to type 1 diabetes: diabetes autoimmunity study in the young (DAISY) J. Clin. Endocrinol. Metab. 89 2004 3896 3902
14. J.L. Gross, M.J. de Azevedo, S.P. Silveiro, L.H. Canani, M.L. Caramori, and T. Zelmanovitz Diabetic nephropathy: diagnosis, prevention, and treatment Diabetes Care 28 2005 164 176
15. A. Kowalski, A. Krikorian, and E.V. Lerma Diabetic nephropathy for the primary care provider: new understandings on early detection and treatment Ochsner J. 14 2014 369 379
16. H.J. Lambers Heerspink, and D. de Zeeuw Debate: PRO position. Should microalbuminuria ever be considered as a renal endpoint in any clinical trial? Am. J. Nephrol. 31 2010 458 461 (discussion 468)
17. J.C. Pickup, S.C. Freeman, and A.J. Sutton Glycaemic control in type 1 diabetes during real time continuous glucose monitoring compared with self monitoring of blood glucose: meta-analysis of randomised controlled trials using individual patient data BMJ 343 2011 d3805
18. Y. Kitis, and O.N. Emiroglu The effects of home monitoring by public health nurse on individuals' diabetes control Appl. Nurs. Res. 19 2006 134 143
19. R. Saxena, B.F. Voight, V. Lyssenko, N.P. Burtt, P.I. de Bakker, H. Chen, J.J. Roix, S. Kathiresan, J.N. Hirschhorn, M.J. Daly, T.E. Hughes, L. Groop, D. Altshuler, P. Almgren, J.C. Florez, J. Meyer, K. Ardlie, K. Bengtsson Bostrom, B. Isomaa, G. Lettre, U. Lindblad, H.N. Lyon, O. Melander, C. Newton-Cheh, P. Nilsson, M. Orho-Melander, L. Rastam, E.K. Speliotes, M.R. Taskinen, T. Tuomi, C. Guiducci, A. Berglund, J. Carlson, L. Gianniny, R. Hackett, L. Hall, J. Holmkvist, E. Laurila, M. Sjogren, M. Sterner, A. Surti, M. Svensson, R. Tewhey, B. Blumenstiel, M. Parkin, M. Defelice, R. Barry, W. Brodeur, J. Camarata, N. Chia, M. Fava, J. Gibbons, B. Handsaker, C. Healy, K. Nguyen, C. Gates, C. Sougnez, D. Gage, M. Nizzari, S.B. Gabriel, G.W. Chirn, Q. Ma, H. Parikh, D. Richardson, D. Ricke, and S. Purcell Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels Science 316 2007 1331 1336
20. E.E. Schadt Molecular networks as sensors and drivers of common human diseases Nature 461 2009 218 223
21. Q. Tian, S.B. Stepaniants, M. Mao, L. Weng, M.C. Feetham, M.J. Doyle, E.C. Yi, H. Dai, V. Thorsson, J. Eng, D. Goodlett, J.P. Berger, B. Gunter, P.S. Linseley, R.B. Stoughton, R. Aebersold, S.J. Collins, W.A. Hanlon, and L.E. Hood Integrated genomic and proteomic analyses of gene expression in Mammalian cells Mol. Cell Proteomics 3 2004 960 969
22. J. Godovac-Zimmermann, and L.R. Brown Perspectives for mass spectrometry and functional proteomics Mass Spectrom. Rev. 20 2001 1 57
23. R. Aebersold, L. Anderson, R. Caprioli, B. Druker, L. Hartwell, and R. Smith Perspective: a program to improve protein biomarker discovery for cancer J. Proteome Res. 4 2005 1104 1109
24. N.L. Anderson, and N.G. Anderson The human plasma proteome: history, character, and diagnostic prospects Mol. Cell Proteomics 1 2002 845 867
25. S. Bencharit, S.S. Baxter, J. Carlson, W.C. Byrd, M.V. Mayo, M.B. Border, H. Kohltfarber, E. Urrutia, E.L. Howard-Williams, S. Offenbacher, M.C. Wu, and J.B. Buse Salivary proteins associated with hyperglycemia in diabetes: a proteomic analysis Mol. Biosyst. 9 2013 2785 2797
26. H.J. Kim, P.K. Kim, H.S. Yoo, and C.W. Kim Comparison of tear proteins between healthy and early diabetic retinopathy patients Clin. Biochem. 45 2012 60 67
27. Y. Ma, C. Yang, Y. Tao, H. Zhou, and Y. Wang Recent technological developments in proteomics shed new light on translational research on diabetic microangiopathy FEBS J. 280 2013 5668 5681
28. D.J. States, G.S. Omenn, T.W. Blackwell, D. Fermin, J. Eng, D.W. Speicher, and S.M. Hanash Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study Nat. Biotechnol. 24 2006 333 338
29. M. Polanski, and N.L. Anderson A list of candidate cancer biomarkers for targeted proteomics Biomark. Insights 1 2007 1 48
30. S. Surinova, R. Schiess, R. Huttenhain, F. Cerciello, B. Wollscheid, and R. Aebersold On the development of plasma protein biomarkers J. Proteome Res. 10 2011 5 16
31. W. Zhi, A. Sharma, S. Purohit, E. Miller, B. Bode, S.W. Anderson, J.C. Reed, R.D. Steed, L. Steed, D. Hopkins, and J.X. She Discovery and validation of serum protein changes in type 1 diabetes patients using high throughput two dimensional liquid chromatography-mass spectrometry and immunoassays Mol. Cell Proteomics 10 2011 (M111 012203)
32. X. Liu, Q. Feng, Y. Chen, J. Zuo, N. Gupta, Y. Chang, and F. Fang Proteomics-based identification of differentially-expressed proteins including galectin-1 in the blood plasma of type 2 diabetic patients J. Proteome Res. 8 2009 1255 1262
33. T.M. Jensen, D.R. Witte, D. Pieragostino, J.N. McGuire, E.D. Schjerning, C. Nardi, A. Urbani, M. Kivimaki, E.J. Brunner, A.G. Tabak, and D. Vistisen Association between protein signals and type 2 diabetes incidence Acta Diabetol. 50 2013 697 704
34. S. Riaz, S.S. Alam, and M.W. Akhtar Proteomic identification of human serum biomarkers in diabetes mellitus type 2 J. Pharm. Biomed. Anal. 51 2010 1103 1107
35. T. Sundsten, B. Zethelius, C. Berne, and P. Bergsten Plasma proteome changes in subjects with Type 2 diabetes mellitus with a low or high early insulin response Clin. Sci. 114 2008 499 507
36. M. Zhou, T.P. Conrads, and T.D. Veenstra Proteomics approaches to biomarker detection Brief. Funct. Genomic. Proteomic. 4 2005 69 75
37. M. Latterich, M. Abramovitz, and B. Leyland-Jones Proteomics: new technologies and clinical applications Eur. J. Cancer 44 2008 2737 2741
38. J. Brand, T. Haslberger, W. Zolg, G. Pestlin, and S. Palme Depletion efficiency and recovery of trace markers from a multiparameter immunodepletion column Proteomics 6 2006 3236 3242
39. H. Zhang, X.J. Li, D.B. Martin, and R. Aebersold Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry Nat. Biotechnol. 21 2003 660 666
40. Y. Liu, R. Huttenhain, S. Surinova, L.C. Gillet, J. Mouritsen, R. Brunner, P. Navarro, and R. Aebersold Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS Proteomics 13 2013 1247 1256
41. B.S. Powell, A.V. Lazarev, G. Carlson, A.R. Ivanov, and D.A. Rozak Pressure cycling technology in systems biology Methods Mol. Biol. 881 2012 27 62
42. D. Lopez-Ferrer, K. Petritis, K.K. Hixson, T.H. Heibeck, R.J. Moore, M.E. Belov, D.G. Camp II, and R.D. Smith Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: proteomics on the fly J. Proteome Res. 7 2008 3276 3281
43. C.B. Fowler, T.J. Waybright, T.D. Veenstra, T.J. O'Leary, and J.T. Mason Pressure-assisted protein extraction: a novel method for recovering proteins from archival tissue for proteomic analysis J. Proteome Res. 11 2012 2602 2608
44. J. Lebastchi, and K.C. Herold Immunologic and metabolic biomarkers of beta-cell destruction in the diagnosis of type 1 diabetes Cold Spring Harb. Perspect. Med. 2 2012 a007708
45. S. Miersch, X. Bian, G. Wallstrom, S. Sibani, T. Logvinenko, C.H. Wasserfall, D. Schatz, M. Atkinson, J. Qiu, and J. LaBaer Serological autoantibody profiling of type 1 diabetes by protein arrays J. Proteomics 94 2013 486 496
46. P. Wang, J.R. Whiteaker, and A.G. Paulovich The evolving role of mass spectrometry in cancer biomarker discovery Cancer Biol. Ther. 8 2009 1083 1094
47. J.M. Schwenk, U. Igel, M. Neiman, H. Langen, C. Becker, A. Bjartell, F. Ponten, F. Wiklund, H. Gronberg, P. Nilsson, and M. Uhlen Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays Mol. Cell Proteomics 9 2010 2497 2507
48. Y. Liu, R. Huttenhain, B. Collins, and R. Aebersold Mass spectrometric protein maps for biomarker discovery and clinical research Expert Rev. Mol. Diagn. 13 2013 811 825
49. T. Rabilloud Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains Proteomics 2 2002 3 10
50. D.M. Maahs, J. Siwy, A. Argiles, M. Cerna, C. Delles, A.F. Dominiczak, N. Gayrard, A. Iphofer, L. Jansch, G. Jerums, K. Medek, H. Mischak, G.J. Navis, J.M. Roob, K. Rossing, P. Rossing, I. Rychlik, E. Schiffer, R.E. Schmieder, T.C. Wascher, B.M. Winklhofer-Roob, L.U. Zimmerli, P. Zurbig, and J.K. Snell-Bergeon Urinary collagen fragments are significantly altered in diabetes: a link to pathophysiology PLoS One 5 2010
51. R. Aebersold, and D.R. Goodlett Mass spectrometry in proteomics Chem. Rev. 101 2001 269 295
52. C.K. Frese, A.F. Altelaar, M.L. Hennrich, D. Nolting, M. Zeller, J. Griep-Raming, A.J. Heck, and S. Mohammed Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos J. Proteome Res. 10 2011 2377 2388
53. M. Bantscheff, M. Schirle, G. Sweetman, J. Rick, and B. Kuster Quantitative mass spectrometry in proteomics: a critical review Anal. Bioanal. Chem. 389 2007 1017 1031
54. P. Mallick, and B. Kuster Proteomics: a pragmatic perspective Nat. Biotechnol. 28 2010 695 709
55. Q. Zhang, T.L. Fillmore, A.A. Schepmoes, T.R. Clauss, M.A. Gritsenko, P.W. Mueller, M. Rewers, M.A. Atkinson, R.D. Smith, and T.O. Metz Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes J. Exp. Med. 210 2013 191 203
56. A.J. Overgaard, T.E. Thingholm, M.R. Larsen, L. Tarnow, P. Rossing, J.N. McGuire, and F. Pociot Quantitative iTRAQ-based proteomic identification of candidate biomarkers for diabetic nephropathy in plasma of type 1 diabetic patients Clin. Proteomics 6 2010 105 114
57. V. Lange, P. Picotti, B. Domon, and R. Aebersold Selected reaction monitoring for quantitative proteomics: a tutorial Mol. Syst. Biol. 4 2008 222
58. P. Picotti, and R. Aebersold Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions Nat. Methods 9 2012 555 566
59. M.A. Kuzyk, D. Smith, J. Yang, T.J. Cross, A.M. Jackson, D.B. Hardie, N.L. Anderson, and C.H. Borchers Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma Mol. Cell Proteomics 8 2009 1860 1877
60. K. Kim, S.J. Kim, H.G. Yu, J. Yu, K.S. Park, I.J. Jang, and Y. Kim Verification of biomarkers for diabetic retinopathy by multiple reaction monitoring J. Proteome Res. 9 2010 689 699
61. C. Krisp, S.A. Randall, M.J. McKay, and M.P. Molloy Towards clinical applications of selected reaction monitoring for plasma protein biomarker studies Proteomics Clin. Appl. 6 2012 42 59
62. J.C. Silva, M.V. Gorenstein, G.Z. Li, J.P. Vissers, and S.J. Geromanos Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition Mol. Cell Proteomics 5 2006 144 156
63. T. Geiger, J. Cox, and M. Mann Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation Mol. Cell Proteomics 9 2010 2252 2261
64. C.R. Weisbrod, J.K. Eng, M.R. Hoopmann, T. Baker, and J.E. Bruce Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification J. Proteome Res. 11 2012 1621 1632
65. L.C. Gillet, P. Navarro, S. Tate, H. Rost, N. Selevsek, L. Reiter, R. Bonner, and R. Aebersold Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis Mol. Cell Proteomics 11 2012 (O111 016717)
66. B.C. Collins, L.C. Gillet, G. Rosenberger, H.L. Rost, A. Vichalkovski, M. Gstaiger, and R. Aebersold Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system Nat. Methods 10 2013 1246 1253
67. J.D. Egertson, A. Kuehn, G.E. Merrihew, N.W. Bateman, B.X. MacLean, Y.S. Ting, J.D. Canterbury, D.M. Marsh, M. Kellmann, V. Zabrouskov, C.C. Wu, and M.J. MacCoss Multiplexed MS/MS for improved data-independent acquisition Nat. Methods 10 2013 744 746
68. Method of the Year 2012 Nat. Methods 10 2013 1
69. A.J. Percy, A.G. Chambers, J. Yang, D.B. Hardie, and C.H. Borchers Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility Biochim. Biophys. Acta 1844 2014 917 926
70. P. Picotti, M. Clement-Ziza, H. Lam, D.S. Campbell, A. Schmidt, E.W. Deutsch, H. Rost, Z. Sun, O. Rinner, L. Reiter, Q. Shen, J.J. Michaelson, A. Frei, S. Alberti, U. Kusebauch, B. Wollscheid, R.L. Moritz, A. Beyer, and R. Aebersold A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis Nature 494 2013 266 270
71. T. Farrah, E.W. Deutsch, G.S. Omenn, D.S. Campbell, Z. Sun, J.A. Bletz, P. Mallick, J.E. Katz, J. Malmstrom, R. Ossola, J.D. Watts, B. Lin, H. Zhang, R.L. Moritz, and R. Aebersold A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas Mol. Cell Proteomics 10 2011 (M110 006353)
72. C. Karlsson, L. Malmstrom, R. Aebersold, and J. Malmstrom Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes Nat. Commun. 3 2012 1301
73. O.T. Schubert, J. Mouritsen, C. Ludwig, H.L. Rost, G. Rosenberger, P.K. Arthur, M. Claassen, D.S. Campbell, Z. Sun, T. Farrah, M. Gengenbacher, A. Maiolica, S.H. Kaufmann, R.L. Moritz, and R. Aebersold The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis Cell Host Microbe 13 2013 602 612.