Shotgun-proteomics-based clinical testing for diagnosis and classification of amyloidosis

Journal of Mass Spectrometry

Volumn 48, Issue 10, 2013, Pages 1067-1077

  Theis, Jason D ^a   Dasari, Surendra ^a   Vrana, Julie A ^a   Kurtin, Paul J ^a   Dogan, Ahmet ^a  

^a Department of Laboratory Medicine and Pathology ^*  (United States)

Author keywords

amyloidosis; clinical; diagnostic test; mutant protein; proteomics; spectrometry; tandem mass

Indexed keywords

AMYLOIDOSIS; CLINICAL; DIAGNOSTIC TESTS; MUTANT PROTEINS; PROTEOMICS; TANDEM MASS;

ASSAYS; CLINICAL LABORATORIES; DISEASES; MOLECULAR BIOLOGY; PROTEINS; RESEARCH LABORATORIES; SPECTROMETRY;

DIAGNOSIS;

AMYLOID PROTEIN; ANTIBODY; BIOLOGICAL MARKER; CATION; PROTEIN;

CLINICAL LABORATORY; CLINICAL PRACTICE; COST BENEFIT ANALYSIS; HUMAN; KIDNEY AMYLOIDOSIS; KIDNEY DISEASE; LABORATORY DIAGNOSIS; MEDICAL TECHNOLOGY; ONCOLOGY; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEOMICS; QUALITY CONTROL; REVIEW; SHOTGUN PROTEOMICS ASSAY; STANDARD;

AMYLOIDOSIS; CLINICAL; DIAGNOSTIC TEST; MUTANT PROTEIN; PROTEOMICS; SPECTROMETRY; TANDEM MASS;

AMYLOID; AMYLOIDOSIS; HUMANS; PROTEOMICS; REPRODUCIBILITY OF RESULTS; TANDEM MASS SPECTROMETRY;

EID: 84885573368     PISSN: 10765174     EISSN: 10969888     Source Type: Journal    
DOI: 10.1002/jms.3264     Document Type: Review

References (62)

1. J. R. Wisniewski, K. Dus, M. Mann,. Proteomic workflow for analysis of archival formalin fixed and paraffin embedded clinical samples to a depth of 10,000 proteins. Proteomics Clin. Appl. 2012, 7 (3-4), 225-33.
2. D. L. Tabb,. Quality assessment for clinical proteomics. Clin. Biochem. 2012, 46 (6), 411-20.
3. M. Kishikawa, T. Nakanishi, A. Miyazaki,;, A. Shimizu, M. Nakazato, K. Kangawa, H. Matsuo,. Simple detection of abnormal serum transthyretin from patients with familial amyloidotic polyneuropathy by high-performance liquid chromatography/electrospray ionization mass spectrometry using material precipitated with specific antiserum. J. Mass Spectrom. 1996, 31 (1), 112-4.
4. R. Theberge, L. Connors, M. Skinner, J. Skare, C. E. Costello,. Characterization of transthyretin mutants from serum using immunoprecipitation, HPLC/electrospray ionization and matrix-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 1999, 71 (2), 452-9.
5. H. R. Bergen 3rd, S. R. Zeldenrust, M. L. Butz, D. S. Snow, P. J. Dyck, C. J. Klein, J. F. O'Brien, S. N. Thibodeau, D. C. Muddiman,. Identification of transthyretin variants by sequential proteomic and genomic analysis. Clin. Chem. 2004, 50 (9), 1544-52.
6. O. Trenchevska, Kamcheva E., D. Nedelkov,. Mass spectrometric immunoassay for quantitative determination of transthyretin and its variants. Proteomics 2011, 11 (18), 3633-41.
7. F. Lavatelli, F. Brambilla, V. Valentini, P. Rognoni, S. Casarini, D. Di Silvestre, V. Perfetti, G. Palladini, G. Sarais, P. Mauri, G. Merlini,. A novel approach for the purification and proteomic analysis of pathogenic immunoglobulin free light chains from serum. Biochim. Biophys. Acta 2011, 1814 (3), 409-19.
8. J. C. Lendoire, P. Trigo, H. Aziz, M. C. Romero, O. Inventarza, Y. Ando, K. Tashima, P. I. Ohlsson, K. Cederquist, G. Holmgren, O. B. Suhr,. Variant transthyretin (TTR) amyloidosis in Argentina. Detection of the trait by electrospray ionization mass spectrometry of lyophilized TTR immunoprecipitate. Scand. J. Clin. Lab. Invest. 1999, 59 (8), 613-8.
9. L. Liao, D. Cheng, J. Wang, D. M. Duong, T. G. Losik, M. Gearing, H. D. Rees, J. J. Lah, A. I. Levey, J. Peng,. Proteomic characterization of postmortem amyloid plaques isolated by laser capture microdissection. J. Biol. Chem. 2004, 279 (35), 37061-8.
10. J. A. Vrana, J. D. Gamez, B. J. Madden, J. D. Theis, H. R. 3rd Bergen, A. Dogan,. Classification of amyloidosis by laser microdissection and mass spectrometry-based proteomic analysis in clinical biopsy specimens. Blood 2009, 114 (24), 4957-9.
11. C. L. Murphy, S. Wang, T. Williams, D. T. Weiss, A. Solomon,. Characterization of systemic amyloid deposits by mass spectrometry. Methods Enzymol. 2006, 412, 48-62.
12. F. Brambilla, F. Lavatelli, D. Di Silvestre, V. Valentini, R. Rossi, G. Palladini, L. Obici, L. Verga, P. Mauri, G. Merlini,. Reliable typing of systemic amyloidoses through proteomic analysis of subcutaneous adipose tissue. Blood 2012, 119 (8), 1844-7.
13. F. Lavatelli, D. H. Perlman, B. Spencer, T. Prokaeva, M. E. McComb, R. Theberge, L. H. Connors, V. Bellotti, D. C. Seldin, G. Merlini, M. Skinner, C. E. Costello,. Amyloidogenic and associated proteins in systemic amyloidosis proteome of adipose tissue. Mol. Cell. Proteomics 2008, 7 (8), 1570-83.
14. E. H. Seeley, R. M. Caprioli,. Molecular imaging of proteins in tissues by mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (47), 18126-31.
15. M. P. Washburn, D. Wolters, J. R. Yates 3rd,. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19 (3), 242-7.
16. R. W. Sprung Jr., J. W. Brock, J. P. Tanksley, M. Li, M. K. Washington, R. J. Slebos, D. C. Liebler,. Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol. Cell. Proteomics 2009, 8 (8), 1988-98.
17. B. L. Hood, T. P. Conrads, T. D. Veenstra,. Unravelling the proteome of formalin-fixed paraffin-embedded tissue. Brief. Funct. Genomic. Proteomic. 2006, 5 (2), 169-75.
18. C. B. Fowler, T. J. Waybright, T. D. Veenstra, T. J. O'Leary, J. T. Mason,. Pressure-assisted protein extraction: a novel method for recovering proteins from archival tissue for proteomic analysis. J. Proteome Res. 2012, 11 (4), 2602-8.
19. J. O. Gustafsson, M. K. Oehler, S. R. McColl, P. Hoffmann,. Citric acid antigen retrieval (CAAR) for tryptic peptide imaging directly on archived formalin-fixed paraffin-embedded tissue. J. Proteome Res. 2010, 9 (9), 4315-28.
20. A. Tanca, D. Pagnozzi, G. P. Burrai, M. Polinas, S. Uzzau, E. Antuofermo, M. F. Addis,. Comparability of differential proteomics data generated from paired archival fresh-frozen and formalin-fixed samples by GeLC-MS/MS and spectral counting. J. Proteomics 2012, 77, 561-76.
21. J. K. Eng, A. L. McCormack, J. R. Yates,. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom 1994, 5, (11), 976-89.
22. D. Fenyo, R. C. Beavis,. A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 2003, 75 (4), 768-74.
23. D. N. Perkins, D. J. Pappin, D. M. Creasy, J. S. Cottrell,. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20 (18), 3551-67.
24. J. E. Elias, W. Haas, B. K. Faherty, S. P. Gygi,. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2005, 2 (9), 667-75.
25. H. Liu, R. G. Sadygov, J. R. Yates 3rd,. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76 (14), 4193-201.
26. J. Ezzelle, I. R. Rodriguez-Chavez, J. M. Darden, M. Stirewalt, N. Kunwar, R. Hitchcock, T. Walter, M. P. D'Souza,. Guidelines on good clinical laboratory practice: bridging operations between research and clinical research laboratories. J. Pharm. Biomed. Anal. 2008, 46 (1), 18-29.
27. A. W. Bell, E. W. Deutsch, C. E. Au, R. E. Kearney, R. Beavis, S. Sechi, T. Nilsson, J. J. Bergeron,. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat. Methods 2009, 6 (6), 423-30.
28. M. Mann,. Comparative analysis to guide quality improvements in proteomics. Nat. Methods 2009, 6 (10), 717-19.
29. K. R. Calvo, L. A. Liotta, E. F. Petricoin,. Clinical proteomics: from biomarker discovery and cell signaling profiles to individualized personal therapy. Biosci. Rep. 2005, 25 (1-2), 107-25.
30. D. C. Liebler,. Summary of United States Human Proteome Organisation (HUPO) symposium entitled "Standardized clinical proteomics platforms". Mol. Cell. Proteomics 2009, 8 (5), 1165-6.
31. W. S. Lane, A. I. Nesvizhskii, B. C. Searle, D. L. Tabb, J. A. Falkner, J. A. Kowalak, S. L. Seymour,. In iPRG2008 Study: Assessing the Quality and Consistency of Protein Reporting on a Common Data Set Reporting on a Common Data Set, Annual Conference of Association of Biomolecular Resources, Salt Lake City, Utah 2008.
32. R. M. Zenka, K. L. Johnson, H. R. Bergen,. Exploring Proteomics Metadata Using Spotfire and a Companion User Interface; Poster. In Exploring Proteomics Metadata Using Spotfire and a Companion User Interface. American Society of Mass Spectrometry, Salt Lake City, Utah, 2011.
33. P. A. Rudnick, K. R. Clauser, L. E. Kilpatrick, D. V. Tchekhovskoi, P. Neta, N. Blonder, D. D. Billheimer, R. K. Blackman, D. M. Bunk, H. L. Cardasis, A. J. Ham, J. D. Jaffe, C. R. Kinsinger, M. Mesri, T. A. Neubert, B. Schilling, D. L. Tabb, T. J. Tegeler, L. Vega-Montoto, A. M. Variyath, M. Wang, P. Wang, J. R. Whiteaker, L. J. Zimmerman, S. A. Carr, S. J. Fisher, B. W. Gibson, A. G. Paulovich, F. E. Regnier, H. Rodriguez, C. Spiegelman, P. Tempst, D. C. Liebler, S. E. Stein,. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol. Cell. Proteomics 2010, 9 (2), 225-41.
34. R. P. Linke,. On typing amyloidosis using immunohistochemistry. Detailled illustrations, review and a note on mass spectrometry. Prog. Histochem. Cytochem. 2012, 47 (2), 61-132.
35. M. D. Benson, S. James, K. Scott, J. J. Liepnieks, B. Kluve-Beckerman,. Leukocyte chemotactic factor 2: A novel renal amyloid protein. Kidney Int. 2008, 74 (2), 218-22.
36. M. D. Benson,. LECT2 amyloidosis. Kidney Int. 2010, 77 (9), 757-9.
37. C. L. Murphy, S. Wang, D. Kestler, C. Larsen, D. Benson, D. T. Weiss, A. Solomon,. Leukocyte chemotactic factor 2 (LECT2)-associated renal amyloidosis: a case series. Am. J. Kidney Dis. 2010, 56 (6), 1100-7.
38. S. H. Nasr, M. E. Fidler, L. D. Cornell, N. Leung, F. G. Cosio, S. S. Sheikh, A. A. Amir, J. A. Vrana, J. D. Theis, A. Dogan, S. Sethi,. Immunotactoid glomerulopathy: clinicopathologic and proteomic study. Nephrol. Dial. Transplant. 2012, 27 (11), 4137-46.
39. S. H. Nasr, S. M. Said, A. M. Valeri, S. Sethi, M. E. Fidler, L. D. Cornell, M. A. Gertz, A. Dispenzieri, F. K. Buadi, J. A. Vrana, J. D. Theis, A. Dogan, N. Leung,. The diagnosis and characteristics of renal heavy-chain and heavy/light-chain amyloidosis and their comparison with renal light-chain amyloidosis. Kidney Int. 2013, 83 (3), 463-70.
40. S. Sethi, J. D. Theis, J. A. Vrana, F. C. Fervenza, A. Sethi, Q. Qian, P. Quint, N. Leung, A. Dogan, S. H. Nasr,. Laser Microdissection and Proteomic Analysis of Amyloidosis, Cryoglobulinemic GN, Fibrillary GN, and Immunotactoid Glomerulopathy. Clin. J. Am. Soc. Nephrol. 2013, 8 (6), 915-921.
41. S. Sethi, J. A. Vrana, J. D. Theis, N. Leung, A. Sethi, S. H. Nasr, F. C. Fervenza, L. D. Cornell, M. E. Fidler, A. Dogan,. Laser microdissection and mass spectrometry-based proteomics aids the diagnosis and typing of renal amyloidosis. Kidney Int. 2012, 82 (2), 226-34.
42. L. Sepiashvili, A. Hui, V. Ignatchenko, W. Shi, S. Su, W. Xu, S. H. Huang, B. O'Sullivan, J. Waldron, J. C. Irish, B. Perez-Ordonez, F. F. Liu, T. Kislinger,. Potentially novel candidate biomarkers for head and neck squamous cell carcinoma identified using an integrated cell line-based discovery strategy. Mol. Cell. Proteomics 2012, 11 (11), 1404-15.
43. E. P. de Jong, H. Xie, G. Onsongo, M. D. Stone, X. B. Chen, J. A. Kooren, E. W. Refsland, R. J. Griffin, F. G. Ondrey, B. Wu, C. T. Le, N. L. Rhodus, J. V. Carlis, T. J. Griffin,. Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions. PLoS One 2010, 5, (6), e11148.
44. S. Hu, M. Arellano, P. Boontheung, J. Wang, H. Zhou, J. Jiang, D. Elashoff, R. Wei, J. A. Loo, D. T. Wong,. Salivary proteomics for oral cancer biomarker discovery. Clin. Cancer Res. 2008, 14 (19), 6246-52.
45. A. Gamez-Pozo, N. I. Ferrer, E. Ciruelos, R. Lopez-Vacas, F. G. Martinez, E. Espinosa, J. A. Vara,. Shotgun proteomics of archival triple-negative breast cancer samples. Proteomics Clin. Appl. 2013, 7 (3-4), 283-91.
46. S. Cha, M. B. Imielinski, T. Rejtar, E. A. Richardson, D. Thakur, D. C. Sgroi, B. L. Karger,. In situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection: annotation by protein set enrichment analysis and gene ontology. Mol. Cell. Proteomics 2010, 9 (11), 2529-44.
47. C. Sandhu, M. Connor, T. Kislinger, J. Slingerland, A. Emili,. Global protein shotgun expression profiling of proliferating mcf-7 breast cancer cells. J. Proteome Res. 2005, 4 (3), 674-89.
48. T. Kikuchi, M. Hassanein, J. M. Amann, Q. Liu, R. J. Slebos, S. M. Rahman, J. M. Kaufman, X. Zhang, M. D. Hoeksema, B. K. Harris, M. Li, Y. Shyr, A. L. Gonzalez, L. J. Zimmerman, D. C. Liebler, P. P. Massion, D. P. Carbone,. In-depth proteomic analysis of nonsmall cell lung cancer to discover molecular targets and candidate biomarkers. Mol. Cell. Proteomics 2012, 11 (10), 916-32.
49. C. Planque, V. Kulasingam, C. R. Smith, K. Reckamp, Goodglick L., E. P. Diamandis,. Identification of five candidate lung cancer biomarkers by proteomics analysis of conditioned media of four lung cancer cell lines. Mol. Cell. Proteomics 2009, 8 (12), 2746-58.
50. H. Kosanam, S. Makawita, B. Judd, A. Newman, E. P. Diamandis,. Mining the malignant ascites proteome for pancreatic cancer biomarkers. Proteomics 2011, 11 (23), 4551-8.
51. R. Chen, S. Pan, E. C. Yi, S. Donohoe, M. P. Bronner, J. D. Potter, D. R. Goodlett, R. Aebersold, T. A. Brentnall,. Quantitative proteomic profiling of pancreatic cancer juice. Proteomics 2006, 6 (13), 3871-9.
52. M. Gronborg, J. Bunkenborg, T. Z. Kristiansen, O. N. Jensen, C. J. Yeo, R. H. Hruban, A. Maitra, M. G. Goggins, A. Pandey,. Comprehensive proteomic analysis of human pancreatic juice. J. Proteome Res. 2004, 3 (5), 1042-55.
53. S. I. Hwang, J. Thumar, D. H. Lundgren, K. Rezaul, V. Mayya, L. Wu, J. Eng, M. E. Wright, D. K. Han,. Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene 2007, 26 (1), 65-76.
54. Y. Kim, V. Ignatchenko, C. Q. Yao, I. Kalatskaya, J. O. Nyalwidhe, R. S. Lance, A. O. Gramolini, D. A. Troyer, L. D. Stein, P. C. Boutros, J. A. Medin, O. J. Semmes, R. R. Drake, T. Kislinger,. Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer. Mol. Cell. Proteomics 2012, 11, (12), 1870-84.
55. S. Elschenbroich, V. Ignatchenko, B. Clarke, S. E. Kalloger, P. C. Boutros, A. O. Gramolini, P. Shaw, I. Jurisica, T. Kislinger,. In-depth proteomics of ovarian cancer ascites: combining shotgun proteomics and selected reaction monitoring mass spectrometry. J. Proteome Res. 2011, 10 (5), 2286-99.
56. M. Montagnana, E. Danese, S. Giudici, M. Franchi, G. C. Guidi, M. Plebani, G. Lippi,. HE4 in ovarian cancer: from discovery to clinical application. Adv. Clin. Chem. 2011, 55, 1-20.
57. M. de Wit, R. J. Fijneman, H. M. Verheul, G. A. Meijer, C. R. Jimenez,. Proteomics in colorectal cancer translational research: Biomarker discovery for clinical applications. Clin. Biochem. 2012, 46 (6), 466-79.
58. G. S. Karagiannis, C. Petraki, I. Prassas, P. Saraon, N. Musrap, A. Dimitromanolakis, E. P. Diamandis,. Proteomic signatures of the desmoplastic invasion front reveal collagen type XII as a marker of myofibroblastic differentiation during colorectal cancer metastasis. Oncotarget 2012, 3 (3), 267-85.
59. J. R. Wisniewski, P. Ostasiewicz, K. Dus, D. F. Zielinska, F. Gnad, M. Mann,. Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol. Syst. Biol. 2012, 8, 611.
60. T. Hembrough, S. Thyparambil, W. L. Liao, M. M. Darfler, J. Abdo, K. M. Bengali, P. Taylor, J. Tong, H. Lara-Guerra, T. K. Waddell, M. F. Moran, M. S. Tsao, D. B. Krizman, J. Burrows,. Selected Reaction Monitoring (SRM) Analysis of Epidermal Growth Factor Receptor (EGFR) in Formalin Fixed Tumor Tissue. Clin Proteomics 2012, 9 (1), 5.
61. N. Azad, M. Yu, B. Davidson, P. Choyke, C. C. Chen, B. J. Wood, A. Venkatesan, R. Henning, K. Calvo, L. Minasian, D. C. Edelman, P. Meltzer, S. M. Steinberg, C. M. Annunziata, E. C. Kohn,. Translational predictive biomarker analysis of the phase 1b sorafenib and bevacizumab study expansion cohort. Mol. Cell. Proteomics 2013, 12 (6), 1621-31.
62. S. D. Sherrod, M. V. Myers, M. Li, J. S. Myers, K. L. Carpenter, B. Maclean, M. J. Maccoss, D. C. Liebler, A. J. Ham,. Label-Free Quantitation of Protein Modifications by Pseudo Selected Reaction Monitoring with Internal Reference Peptides. J. Proteome Res. 2012, 11 (6), 3467-79.