Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics

Science Translational Medicine

Volumn 4, Issue 142, 2012, Pages

  Hüttenhain, Ruth ^a,b   Soste, Martin ^a   Selevsek, Nathalie ^a   Röst, Hannes ^a,c   Sethi, Atul ^a,c   Carapito, Christine ^a   Farrah, Terry ^d   Deutsch, Eric W ^d   Kusebauch, Ulrike ^d   Moritz, Robert L ^d   Niméus Malmström, Emma ^e   Rinner, Oliver ^f   Aebersold, Ruedi ^a,b,c  

^a ETH ZURICH   (Switzerland)

^b Competence Center for Systems Physiology and Metabolic Diseases ^*  (Switzerland)

^c UNIVERSITY OF ZURICH   (Switzerland)

^d INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^e LUND UNIVERSITY   (Sweden)

^f Biognosys AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN A1; BETA 2 MICROGLOBULIN; PREALBUMIN; PROTEOME; TRANSFERRIN; TUMOR ANTIGEN; TUMOR PROTEIN;

ACCURACY; ARTICLE; BODY FLUID; CARCINOGENESIS; CLINICAL ARTICLE; CONTROLLED STUDY; DISEASE ACTIVITY; DISEASE ASSOCIATION; FEMALE; GENE MUTATION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN TISSUE; INVESTIGATIVE PROCEDURES; MALE; MASS SPECTROMETRY; MOLECULAR PATHOLOGY; NEOPLASM; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN BLOOD LEVEL; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN TARGETING; PROTEIN URINE LEVEL; PROTEOMICS; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; SELECTED REACTION MONITORING; SENSITIVITY AND SPECIFICITY;

BODY FLUIDS; COHORT STUDIES; FEMALE; GENES, NEOPLASM; HUMANS; MUTATION; NEOPLASM PROTEINS; NEOPLASMS; OVARIAN NEOPLASMS; PEPTIDES; PROTEIN INTERACTION MAPS; PROTEOMICS; REPRODUCIBILITY OF RESULTS; TUMOR MARKERS, BIOLOGICAL;

EID: 84863923380     PISSN: 19466234     EISSN: 19466242     Source Type: Journal    
DOI: 10.1126/scitranslmed.3003989     Document Type: Article

References (80)

1. J. A. Ludwig, J. N. Weinstein, Biomarkers in cancer staging, prognosis and treatment selection. Nat. Rev. Cancer 5, 845-856 (2005).
2. R. Schiess, B. Wollscheid, R. Aebersold, Targeted proteomic strategy for clinical biomarker discovery. Mol. Oncol. 3, 33-44 (2009).
3. N. L. Anderson, N. G. Anderson, T. W. Pearson, C. H. Borchers, A. G. Paulovich, S. D. Patterson, M. Gillette, R. Aebersold, S. A. Carr, A human proteome detection and quantitation project. Mol. Cell. Proteomics 8, 883-886 (2009).
4. N. Rifai, M. A. Gillette, S. A. Carr, Protein biomarker discovery and validation: The long and uncertain path to clinical utility. Nat. Biotechnol. 24, 971-983 (2006).
5. S. Surinova, R. Schiess, R. Hüttenhain, F. Cerciello, B. Wollscheid, R. Aebersold, On the development of plasma protein biomarkers. J. Proteome Res. 10, 5-16 (2011).
6. N. Selevsek, M. Matondo, M. S. Carbayo, R. Aebersold, B. Domon, Systematic quantification of peptides/proteins in urine using selected reaction monitoring. Proteomics 11, 1135-1147 (2011).
7. N. L. Anderson, N. G. Anderson, The human plasma proteome: History, character, and diagnostic prospects. Mol. Cell. Proteomics 1, 845-867 (2002).
8. N. L. Anderson, The clinical plasma proteome: A survey of clinical assays for proteins in plasma and serum. Clin. Chem. 56, 177-185 (2010).
9. R. Hüttenhain, J. Malmström, P. Picotti, R. Aebersold, Perspectives of targeted mass spectrometry for protein biomarker verification. Curr. Opin. Chem. Biol. 13, 518-525 (2009).
10. J. R. Whiteaker, C. Lin, J. Kennedy, L. Hou, M. Trute, I. Sokal, P. Yan, R. M. Schoenherr, L. Zhao, U. J. Voytovich, K. S. Kelly-Spratt, A. Krasnoselsky, P. R. Gafken, J. M. Hogan, L. A. Jones, P. Wang, L. Amon, L. A. Chodosh, P. S. Nelson, M. W. McIntosh, C. J. Kemp, A. G. Paulovich, A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat. Biotechnol. 29, 625-634 (2011).
11. A. G. Paulovich, J. R. Whiteaker, A. N. Hoofnagle, P. Wang, The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline. Proteomics Clin. Appl. 2, 1386-1402 (2008).
12. T. Ideker, R. Sharan, Protein networks in disease. Genome Res. 18, 644-652 (2008).
13. H. Y. Chuang, E. Lee, Y. T. Liu, D. Lee, T. Ideker, Network-based classification of breast cancer metastasis. Mol. Syst. Biol. 3, 140 (2007).
14. R. K. Nibbe, M. Koyutürk, M. R. Chance, An integrative -omics approach to identify functional sub-networks in human colorectal cancer. PLoS Comput. Biol. 6, e1000639 (2010).
15. E. Cerami, E. Demir, N. Schultz, B. S. Taylor, C. Sander, Automated network analysis identifies core pathways in glioblastoma. PLoS One 5, e8918 (2010).
16. G. Wu, X. Feng, L. Stein, A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 11, R53 (2010).
17. K. X. Zhang, B. F. Ouellette, CAERUS: Predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data. PLoS Comput. Biol. 7, e1001114 (2011).
18. B. Domon, R. Aebersold, Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 28, 710-721 (2010).
19. V. Lange, P. Picotti, B. Domon, R. Aebersold, Selected reaction monitoring for quantitative proteomics: A tutorial. Mol. Syst. Biol. 4, 222 (2008).
20. T. A. Addona, X. Shi, H. Keshishian, D. R. Mani, M. Burgess, M. A. Gillette, K. R. Clauser, D. Shen, G. D. Lewis, L. A. Farrell, M. A. Fifer, M. S. Sabatine, R. E. Gerszten, S. A. Carr, A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. Nat. Biotechnol. 29, 635-643 (2011).
21. J. R. Whiteaker, H. Zhang, L. Zhao, P. Wang, K. S. Kelly-Spratt, R. G. Ivey, B. D. Piening, L. C. Feng, E. Kasarda, K. E. Gurley, J. K. Eng, L. A. Chodosh, C. J. Kemp, M. W. McIntosh, A. G. Paulovich, Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J. Proteome Res. 6, 3962-3975 (2007).
22. I. Cima, R. Schiess, P. Wild, M. Kaelin, P. Schüffler, V. Lange, P. Picotti, R. Ossola, A. Templeton, O. Schubert, T. Fuchs, T. Leippold, S. Wyler, J. Zehetner, W. Jochum, J. Buhmann, T. Cerny, H. Moch, S. Gillessen, R. Aebersold, W. Krek, Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer. Proc. Natl. Acad. Sci. U.S.A. 108, 3342-3347 (2011).
23. P. Picotti, O. Rinner, R. Stallmach, F. Dautel, T. Farrah, B. Domon, H. Wenschuh, R. Aebersold, High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Methods 7, 43-46 (2010).
24. T. A. Addona, S. E. Abbatiello, B. Schilling, S. J. Skates, D. R. Mani, D. M. Bunk, C. H. Spiegelman, L. J. Zimmerman, A. J. Ham, H. Keshishian, S. C. Hall, S. Allen, R. K. Blackman, C. H. Borchers, C. Buck, H. L. Cardasis, M. P. Cusack, N. G. Dodder, B. W. Gibson, J. M. Held, T. Hiltke, A. Jackson, E. B. Johansen, C. R. Kinsinger, J. Li, M. Mesri, T. A. Neubert, R. K. Niles, T. C. Pulsipher, D. Ransohoff, H. Rodriguez, P. A. Rudnick, D. Smith, D. L. Tabb, T. J. Tegeler, A.M. Variyath, L. J. Vega-Montoto, Å. Wahlander, S. Waldemarson, M. Wang, J. R. Whiteaker, L. Zhao, N. L. Anderson, S. J. Fisher, D. C. Liebler, A. G. Paulovich, F. E. Regnier, P. Tempst, S. A. Carr, Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 27, 633-641 (2009).
25. P. Picotti, H. Lam, D. Campbell, E. W. Deutsch, H. Mirzaei, J. Ranish, B. Domon, R. Aebersold, A database of mass spectrometric assays for the yeast proteome. Nat. Methods 5, 913-914 (2008).
26. L. Reiter, O. Rinner, P. Picotti, R. Hüttenhain, M. Beck, M. Y. Brusniak, M. O. Hengartner, R. Aebersold, mProphet: Automated data processing and statistical validation for largescale SRM experiments. Nat. Methods 8, 430-435 (2011).
27. C. Y. Chang, P. Picotti, R. Hüttenhain, V. Heinzelmann-Schwarz, M. Jovanovic, R. Aebersold, O. Vitek, Protein significance analysis in selected reaction monitoring (SRM) measurements. Mol. Cell. Proteomics 11, M111.014662 (2012).
28. M. Polanski, N. L. Anderson, A list of candidate cancer biomarkers for targeted proteomics. Biomark. Insights 1, 1-48 (2007).
29. A. L. Barabási, N. Gulbahce, J. Loscalzo, Network medicine: A network-based approach to human disease. Nat. Rev. Genet. 12, 56-68 (2011).
30. L. D. Wood, D. W. Parsons, S. Jones, J. Lin, T. Sjöblom, R. J. Leary, D. Shen, S. M. Boca, T. Barber, J. Ptak, N. Silliman, S. Szabo, Z. Dezso, V. Ustyanksky, T. Nikolskaya, Y. Nikolsky, R. Karchin, P. A. Wilson, J. S. Kaminker, Z. Zhang, R. Croshaw, J. Willis, D. Dawson, M. Shipitsin, J. K. Willson, S. Sukumar, K. Polyak, B. H. Park, C. L. Pethiyagoda, P. V. Pant, D. G. Ballinger, A. B. Sparks, J. Hartigan, D. R. Smith, E. Suh, N. Papadopoulos, P. Buckhaults, S. D. Markowitz, G. Parmigiani, K. W. Kinzler, V. E. Velculescu, B. Vogelstein, The genomic landscapes of human breast and colorectal cancers. Science 318, 1108-1113 (2007).
31. S. Jones, T. L. Wang, I. M. Shih, T. L. Mao, K. Nakayama, R. Roden, R. Glas, D. Slamon, L. A. Diaz Jr., B. Vogelstein, K. W. Kinzler, V. E. Velculescu, N. Papadopoulos, Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330, 228-231 (2010).
32. D. W. Parsons, S. Jones, X. Zhang, J. C. Lin, R. J. Leary, P. Angenendt, P. Mankoo, H. Carter, I. M. Siu, G. L. Gallia, A. Olivi, R. McLendon, B. A. Rasheed, S. Keir, T. Nikolskaya, Y. Nikolsky, D. A. Busam, H. Tekleab, L. A. Diaz Jr., J. Hartigan, D. R. Smith, R. L. Strausberg, S. K. Marie, S. M. Shinjo, H. Yan, G. J. Riggins, D. D. Bigner, R. Karchin, N. Papadopoulos, G. Parmigiani, B. Vogelstein, V. E. Velculescu, K. W. Kinzler, An integrated genomic analysis of human glioblastoma multiforme. Science 321, 1807-1812 (2008).
33. D. W. Parsons, M. Li, X. Zhang, S. Jones, R. J. Leary, J. C. Lin, S. M. Boca, H. Carter, J. Samayoa, C. Bettegowda, G. L. Gallia, G. I. Jallo, Z. A. Binder, Y. Nikolsky, J. Hartigan, D. R. Smith, D. S. Gerhard, D. W. Fults, S. Vandenberg, M. S. Berger, S. K. Marie, S. M. Shinjo, C. Clara, P. C. Phillips, J. E. Minturn, J. A. Biegel, A. R. Judkins, A. C. Resnick, P. B. Storm, T. Curran, Y. He, B. A. Rasheed, H. S. Friedman, S. T. Keir, R. McLendon, P. A. Northcott, M. D. Taylor, P. C. Burger, G. J. Riggins, R. Karchin, G. Parmigiani, D. D. Bigner, H. Yan, N. Papadopoulos, B. Vogelstein, K. W. Kinzler, V. E. Velculescu, The genetic landscape of the childhood cancer medulloblastoma. Science 331, 435-439 (2011).
34. S. Jones, X. Zhang, D. W. Parsons, J. C. Lin, R. J. Leary, P. Angenendt, P. Mankoo, H. Carter, H. Kamiyama, A. Jimeno, S. M. Hong, B. Fu, M. T. Lin, E. S. Calhoun, M. Kamiyama, K. Walter, T. Nikolskaya, Y. Nikolsky, J. Hartigan, D. R. Smith, M. Hidalgo, S. D. Leach, A. P. Klein, E.M. Jaffee, M. Goggins, A. Maitra, C. Iacobuzio-Donahue, J. R. Eshleman, S. E. Kern, R. H. Hruban, R. Karchin, N. Papadopoulos, G. Parmigiani, B. Vogelstein, V. E. Velculescu, K. W. Kinzler, Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321, 1801-1806 (2008).
35. Y. Jiao, C. Shi, B. H. Edil, R. F. De Wilde, D. S. Klimstra, A. Maitra, R. D. Schulick, L. H. Tang, C. L. Wolfgang, M. A. Choti, V. E. Velculescu, L. A. Diaz Jr., B. Vogelstein, K. W. Kinzler, R. H. Hruban, N. Papadopoulos, DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors. Science 331, 1199-1203 (2011).
36. R. Wu, N. Hendrix-Lucas, R. Kuick, Y. Zhai, D. R. Schwartz, A. Akyol, S. Hanash, D. E. Misek, H. Katabuchi, B. O. Williams, E. R. Fearon, K. R. Cho, Mouse model of human ovarian endometrioid adenocarcinoma based on somatic defects in the Wnt/b-catenin and PI3K/Pten signaling pathways. Cancer Cell 11, 321-333 (2007).
37. R. Milo, R. Kashtan, S. Itzkowitz, M. E. J. Newman, U. Alon, On the uniform generation of random graphs with prescribed degree sequences. arXiv:cond-mat/0312028v2 [cond-mat. stat-mech] (2004).
38. B. Kuster, M. Schirle, P. Mallick, R. Aebersold, Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol. 6, 577-583 (2005).
39. P. Mallick, M. Schirle, S. S. Chen, M. R. Flory, H. Lee, D. Martin, J. Ranish, B. Raught, R. Schmitt, T. Werner, B. Kuster, R. Aebersold, Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25, 125-131 (2007).
40. E. W. Deutsch, J. K. Eng, H. Zhang, N. L. King, A. I. Nesvizhskii, B. Lin, H. Lee, E. C. Yi, R. Ossola, R. Aebersold, Human Plasma PeptideAtlas. Proteomics 5, 3497-3500 (2005).
41. 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, R. Aebersold, A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol. Cell. Proteomics 10, M110.006353 (2011).
42. M. Beck, A. Schmidt, J. Malmstroem, M. Claassen, A. Ori, A. Szymborska, F. Herzog, O. Rinner, J. Ellenberg, R. Aebersold, The quantitative proteome of a human cell line. Mol. Syst. Biol. 7, 549 (2011).
43. V. A. Fusaro, D. R. Mani, J. P. Mesirov, S. A. Carr, Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat. Biotechnol. 27, 190-198 (2009).
44. C. Escher, L. Reiter, B. MacLean, R. Ossola, F. Herzog, J. Chilton, M. J. MacCoss, O. Rinner, Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 12, 1111-1121 (2012).
45. J. Sherman, M. J. McKay, K. Ashman, M. P. Molloy, How specific is my SRM?: The issue of precursor and product ion redundancy. Proteomics 9, 1120-1123 (2009).
46. M. W. Duncan, A. L. Yergey, S. D. Patterson, Quantifying proteins by mass spectrometry: The selectivity of SRM is only part of the problem. Proteomics 9, 1124-1127 (2009).
47. D. W. Huang, B. T. Sherman, R. A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2008).
48. D. W. Huang, B. T. Sherman, R. A. Lempicki, Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1-13 (2009).
49. J. Adachi, C. Kumar, Y. Zhang, J. V. Olsen, M. Mann, The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol. 7, R80 (2006).
50. H. Röst, L. Malmström, R. Aebersold, A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol. Cell. Proteomics M111.013045 (2012).
51. J. Sherman, M. J. McKay, K. Ashman, M. P. Molloy, Unique ion signature mass spectrometry, a deterministic method to assign peptide identity. Mol. Cell. Proteomics 8, 2051-2062 (2009).
52. E. T. Fung, A recipe for proteomics diagnostic test development: The OVA1 test, from biomarker discovery to FDA clearance. Clin. Chem. 56, 327-329 (2010).
53. Z. Zhang, D. W. Chan, The road from discovery to clinical diagnostics: Lessons learned from the first FDA-cleared in vitro diagnostic multivariate index assay of proteomic biomarkers. Cancer Epidemiol. Biomarkers Prev. 19, 2995-2999 (2010).
54. D. Bell, A. Berchuck, M. Birrer, J. Chien, D. Cramer, F. Dao, R. Dhir, P. Disaia, H. Gabra, P. Glenn, A. Godwin, J. Gross, L. Hartmann, M. Huang, D. Huntsman, M. Iacocca, M. Imielinski, S. Kalloger, B. Karlan, D. Levine, G. Mills, C. Morrison, D. Mutch, N. Olvera, S. Orsulic, K. Park, N. Petrelli, B. Rabeno, J. Rader, B. Sikic, K. Smith-Mccune, A. Sood, D. Bowtell, R. Penny, J. Testa, K. Chang, H. Dinh, J. Drummond, G. Fowler, P. Gunaratne, A. Hawes, C. Kovar, L. Lewis, M. Morgan, I. Newsham, J. Santibanez, J. Reid, L. Trevino, Y. Wu, M. Wang, D. Muzny, D. Wheeler, R. Gibbs, G. Getz, M. Lawrence, K. Cibulskis, A. Sivachenko, C. Sougnez, D. Voet, J. Wilkinson, T. Bloom, K. Ardlie, T. Fennell, J. Baldwin, S. Gabriel, E. Lander, L. Ding, R. Fulton, D. Koboldt, M. Mclellan, T. Wylie, J. Walker, M. O'Laughlin, D. Dooling, L. Fulton, R. Abbott, N. Dees, Q. Zhang, C. Kandoth, M. Wendl, W. Schierding, D. Shen, C. Harris, H. Schmidt, J. Kalicki, K. Delehaunty, C. Fronick, R. Demeter, L. Cook, J. Wallis, L. Lin, V. Magrini, J. Hodges, J. Eldred, S. Smith, C. Pohl, F. Vandin, B. Raphael, G. Weinstock, E. Mardis, R. Wilson, M. Meyerson, W. Winckler, G. Getz, R. Verhaak, S. Carter, C. Mermel, G. Saksena, H. Nguyen, R. Onofrio, M. Lawrence, D. Hubbard, S. Gupta, A. Crenshaw, A. Ramos, K. Ardlie, L. Chin, A. Protopopov, J. Zhang, T. Kim, I. Perna, Y. Xiao, H. Zhang, G. Ren, N. Sathiamoorthy, R. Park, E. Lee, P. Park, R. Kucherlapati, D. Absher, L. Waite, G. Sherlock, J. Brooks, J. Li, J. Xu, R. Myers, P. Laird, L. Cope, J. Herman, H. Shen, D. Weisenberger, H. Noushmehr, F. Pan, T. Triche Jr., B. Berman, D. Van Den Berg, J. Buckley, S. Baylin, P. Spellman, E. Purdom, P. Neuvial, H. Bengtsson, L. Jakkula, S. Durinck, J. Han, S. Dorton, H. Marr, Y. Choi, V. Wang, N. Wang, J. Ngai, J. Conboy, B. Parvin, H. Feiler, T. Speed, J. Gray, D. Levine, N. Socci, Y. Liang, B. Taylor, N. Schultz, L. Borsu, A. Lash, C. Brennan, A. Viale, C. Sander, M. Ladanyi, K. Hoadley, S. Meng, Y. Du, Y. Shi, L. Li, Y. Turman, D. Zang, E. Helms, S. Balu, X. Zhou, J. Wu, M. Topal, D. Hayes, C. Perou, G. Getz, D. Voet, G. Saksena, J. Zhang, H. Zhang, C. Wu, S. Shukla, K. Cibulskis, M. Lawrence, A. Sivachenko, R. Jing, R. Park, Y. Liu, P. Park, M. Noble, L. Chin, H. Carter, D. Kim, R. Karchin, P. Spellman, E. Purdom, P. Neuvial, H. Bengtsson, S. Durinck, J. Han, J. Korkola, L. Heiser, R. Cho, Z. Hu, B. Parvin, T. Speed, J. Gray, N. Schultz, E. Cerami, B. Taylor, A. Olshen, B. Reva, Y. Antipin, R. Shen, P. Mankoo, R. Sheridan, G. Ciriello, W. Chang, J. Bernanke, L. Borsu, D. Levine, M. Ladanyi, C. Sander, D. Haussler, C. Benz, J. Stuart, S. Benz, J. Sanborn, C. Vaske, J. Zhu, C. Szeto, G. Scott, C. Yau, K. Hoadley, Y. Du, S. Balu, D. Hayes, C. Perou, M. Wilkerson, N. Zhang, R. Akbani, K. Baggerly, W. Yung, G. Mills, J. Weinstein, R. Penny, T. Shelton, D. Grimm, M. Hatfield, S. Morris, P. Yena, P. Rhodes, M. Sherman, J. Paulauskis, S. Millis, A. Kahn, J. Greene, R. Sfeir, M. Jensen, J. Chen, J. Whitmore, S. Alonso, J. Jordan, A. Chu, J. Zhang, A. Barker, C. Compton, G. Eley, M. Ferguson, P. Fielding, D. Gerhard, R. Myles, C. Schaefer, K. Mills Shaw, J. Vaught, J. Vockley, P. Good, M. Guyer, B. Ozenberger, J. Peterson, E. Thomson, Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011).
55. Z. Zhang, R. C. Bast Jr., Y. Yu, J. Li, L. J. Sokoll, A. J. Rai, J. M. Rosenzweig, B. Cameron, Y. Y. Wang, X. Y. Meng, A. Berchuck, C. Van Haaften-Day, N. F. Hacker, H. W. de Bruijn, A. G. van der Zee, I. J. Jacobs, E. T. Fung, D. W. Chan, Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res. 64, 5882-5890 (2004).
56. A. J. Rai, Z. Zhang, J. Rosenzweig, I. Shih, T. Pham, E. T. Fung, L. J. Sokoll, D. W. Chan, Proteomic approaches to tumor marker discovery. Arch. Pathol. Lab. Med. 126, 1518-1526 (2002).
57. T. Farrah, E. W. Deutsch, R. Kreisberg, Z. Sun, D. S. Campbell, L. Mendoza, U. Kusebauch, M. Y. Brusniak, R. Hüttenhain, R. Schiess, N. Selevsek, R. Aebersold, R. L. Moritz, PASSEL: The PeptideAtlas SRM Experiment Library. Proteomics 12, 1170-1175 (2012).
58. J. R. Whiteaker, H. Zhang, J. K. Eng, R. Fang, B. D. Piening, L.-C. Feng, T. D. Lorentzen, R. M. Schoenherr, J. F. Keane, T. Holzman, M. Fitzgibbon, C. Lin, H. Zhang, K. Cooke, T. Liu, D. G. Camp II, L. Anderson, J. Watts, R. D. Smith, M. W. McIntosh, A. G. Paulovich, Head-to-head comparison of serum fractionation techniques. J. Proteome Res. 6, 828-836 (2007).
59. C. Tu, P. A. Rudnick, M. Y. Martinez, K. L. Cheek, S. E. Stein, R. J. C. Slebos, D. C. Liebler, Depletion of abundant plasma proteins and limitations of plasma proteomics. J. Proteome Res. 9, 4982-4991 (2010).
60. J. Stahl-Zeng, V. Lange, R. Ossola, K. Eckhardt, W. Krek, R. Aebersold, B. Domon, High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 6, 1809-1817 (2007).
61. H. Keshishian, T. Addona, M. Burgess, E. Kuhn, S. Carr, Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 6, 2212-2229 (2007).
62. E. Kuhn, T. Addona, H. Keshishian, M. Burgess, D. R. Mani, R. T. Lee, M. S. Sabatine, R. E. Gerszten, S. A. Carr, Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin. Chem. 55, 1108-1117 (2009).
63. A. Luchini, D. H. Geho, B. Bishop, D. Tran, C. Xia, R. L. Dufour, C. D. Jones, V. Espina, A. Patanarut, W. Zhou, M. M. Ross, A. Tessitore, E. F. Petricoin III, L. A. Liotta, Smart hydrogel particles: Biomarker harvesting: One-step affinity purification, size exclusion, and protection against degradation. Nano Lett. 8, 350-361 (2008).
64. C. Fredolini, F. Meani, K. A. Reeder, S. Rucker, A. Patanarut, P. J. Botterell, B. Bishop, C. Longo, V. Espina, E. F. Petricoin III, L. A. Liotta, A. Luchini, Concentration and preservation of very low abundance biomarkers in urine, such as human growth hormone (hGH), by Cibacron Blue F3G-A loaded hydrogel particles. Nano Res. 1, 502-518 (2008).
65. E. Bellei, S. Bergamini, E. Monari, L. I. Fantoni, A. Cuoghi, T. Ozben, A. Tomasi, High-abundance proteins depletion for serum proteomic analysis: Concomitant removal of non-targeted proteins. Amino Acids 40, 145-156 (2011).
66. A. M. Edwards, R. Isserlin, G. D. Bader, S. V. Frye, T. M. Willson, F. H. Yu, Too many roads not taken. Nature 470, 163-165 (2011).
67. R. Haw, H. Hermjakob, P. D'Eustachio, L. Stein, Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics 11, 3598-3613 (2011).
68. P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, T. Ideker, Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003).
69. O. V. Krokhin, Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: Application to 300- and 100-Å pore size C18 sorbents. Anal. Chem. 78, 7785-7795 (2006).
70. O. V. Krokhin, S. Ying, J. P. Cortens, D. Ghosh, V. Spicer, W. Ens, K. G. Standing, R. C. Beavis, J. A. Wilkins, Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS. Anal. Chem. 78, 6265-6269 (2006).
71. H. Wenschuh, R. Volkmer-Engert, M. Schmidt, M. Schulz, J. Schneider-Mergener, U. Reineke, Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides. Biopolymers 55, 188-206 (2000).
72. R. Frank, The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports - Principles and applications. J. Immunol. Methods 267, 13-26 (2002).
73. L. M. Amon, W. Law, M. P. Fitzgibbon, J. A. Gross, K. O'Briant, A. Peterson, C. Drescher, D. B. Martin, M. McIntosh, Integrative proteomic analysis of serum and peritoneal fluids helps identify proteins that are up-regulated in serum of women with ovarian cancer. PLoS One 5, e11137 (2010).
74. C. Kuk, V. Kulasingam, C. G. Gunawardana, C. R. Smith, I. Batruch, E. P. Diamandis, Mining the ovarian cancer ascites proteome for potential ovarian cancer biomarkers. Mol. Cell. Proteomics 8, 661-669 (2009).
75. K. L. Boylan, J. D. Andersen, L. B. Anderson, L. Higgins, A. P. Skubitz, Quantitative proteomic analysis by iTRAQ for the identification of candidate biomarkers in ovarian cancer serum. Proteome Sci. 8, 31 (2010).
76. F. D. Begum, E. Høgdall, S. K. Kjaer, J. Blaakaer, I. J. Christensen, L. Christensen, C. Høgdall, Preoperative serum tetranectin, CA125 and menopausal status used as single markers in screening and in a risk assessment index (RAI) in discriminating between benign and malignant ovarian tumors. Gynecol. Oncol. 113, 221-227 (2009).
77. H. Gadomska, B. Grzechocińska, J. Janecki, G. Nowicka, M. Powolny, L. Marianowski, Serum lipids concentration in women with benign and malignant ovarian tumours. Eur. J. Obstet. Gynecol. Reprod. Biol. 120, 87-90 (2005).
78. V. M. Faça, A. P. Ventura, M. P. Fitzgibbon, S. R. Pereira-Faça, S. J. Pitteri, A. E. Green, R. C. Ireton, Q. Zhang, H. Wang, K. C. O'Briant, C.W. Drescher, M. Schummer, M.W. McIntosh, B. S. Knudsen, S. M. Hanash, Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains. PLoS One 3, e2425 (2008).
79. C. G. Gunawardana, C. Kuk, C. R. Smith, I. Batruch, A. Soosaipillai, E. P. Diamandis, Comprehensive analysis of conditioned media from ovarian cancer cell lines identifies novel candidate markers of epithelial ovarian cancer. J. Proteome Res. 8, 4705-4713 (2009).
80. S. Waldemarson, M. Krogh, A. Alaiya, U. Kirik, K. Schedvins, G. Auer, K. M. Hansson, R. Ossola, R. Aebersold, H. Lee, J. Malmström, P. James, Protein expression changes in ovarian cancer during the transition from benign to malignant. J. Proteome Res. 11, 2876-2889 (2012).