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1. Farrah, T.; Deutsch, E. W.; Omenn, G. S.; Campbell, D. S.; Sun, Z.; Bletz, J. A.; Mallick, P.; Katz, J. E.; Malmstrom, J.; Ossola, R.; Watts, J. D.; Lin, B.; Zhang, H.; Moritz, R. L.; Aebersold, R. H. (2011). A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics. [PubMed]
2. Lee, H. J.; Na, K.; Kwon, M. S.; Park, T.; Kim, K. S.; Kim, H.; Paik, Y. K. (2011). A new versatile peptide-based size exclusion chromatography platform for global profiling and quantitation of candidate biomarkers in hepatocellular carcinoma specimens. Proteomics. 11, 1976-1984. [PubMed]
3. Millioni, R.; Tolin, S.; Puricelli, L.; Sbrignadello, S.; Fadini, G. P.; Tessari, P.; Arrigoni, G. (2011). High abundance proteins depletion vs low abundance proteins enrichment: comparison of methods to reduce the plasma proteome complexity. PLoS One. 6, e19603. [PubMed]
4. Jeong, S. K.; Lee, E. Y.; Cho, J. Y.; Lee, H. J.; Jeong, A. S.; Cho, S. Y.; Paik, Y. K. (2010). Data management and functional annotation of the Korean reference plasma proteome. Proteomics. 10, 1250-1255. [PubMed]
5. Zheng, X.; Wu, S. L.; Hincapie, M.; Hancock, W. S. (2009). Study of the human plasma proteome of rheumatoid arthritis. J Chromatogr A. 1216, 3538-3545. [PubMed]
6. Anderson, N. L.; Anderson, N. G.; Pearson, T. W.; Borchers, C. H.; Paulovich, A. G.; Patterson, S. D.; Gillette, M.; Aebersold, R.; Carr, S. A. (2009). A human proteome detection and quantitation project. Mol Cell Proteomics. 8, 883-886. [PubMed]
7. Saha, S.; Harrison, S. H.; Chen, J. Y. (2009). Dissecting the human plasma proteome and inflammatory response biomarkers. Proteomics. 9, 470-484. [PubMed]
8. Schenk, S.; Schoenhals, G. J.; de Souza, G.; Mann, M. (2008). A high confidence, manually validated human blood plasma protein reference set. BMC Med Genomics. 1, 41. [PubMed]
9. Hortin, G. L.; Sviridov, D.; Anderson, N. L. (2008). High-abundance polypeptides of the human plasma proteome comprising the top 4 logs of polypeptide abundance. Clin Chem. 54, 1608-1616. [PubMed]
10. Zhang, Q.; Tang, N.; Schepmoes, A. A.; Phillips, L. S.; Smith, R. D.; Metz, T. O. (2008). Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes. J Proteome Res. 7, 2025-2032. [PubMed]
11. Liu, X.; Valentine, S. J.; Plasencia, M. D.; Trimpin, S.; Naylor, S.; Clemmer, D. E. (2007). Mapping the human plasma proteome by SCX-LC-IMS-MS. J Am Soc Mass Spectrom. 18, 1249-1264. [PubMed]
12. Zhang, H.; Liu, A. Y.; Loriaux, P.; Wollscheid, B.; Zhou, Y.; Watts, J. D.; Aebersold, R. (2007). Mass spectrometric detection of tissue proteins in plasma. Mol Cell Proteomics. 6, 64-71. [PubMed]
13. Sennels, L.; Salek, M.; Lomas, L.; Boschetti, E.; Righetti, P. G.; Rappsilber, J. (2007). Proteomic analysis of human blood serum using peptide library beads. J Proteome Res. 6, 4055-4062. [PubMed]
14. Omenn, G. S. (2007). THE HUPO Human Plasma Proteome Project. Proteomics Clin Appl. 1, 769-779. [PubMed]
15. Stahl-Zeng, J.; Lange, V.; Ossola, R.; Eckhardt, K.; Krek, W.; Aebersold, R.; Domon, B. (2007). High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics. 6, 1809-1817. [PubMed]
16. Hagglund, P.; Matthiesen, R.; Elortza, F.; Hojrup, P.; Roepstorff, P.; Jensen, O. N.; Bunkenborg, J. (2007). An enzymatic deglycosylation scheme enabling identification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins. J Proteome Res. 6, 3021-3031. [PubMed]
17. Zhou, Y.; Aebersold, R.; Zhang, H. (2007). Isolation of N-linked glycopeptides from plasma. Anal Chem. 79, 5826-5837. [PubMed]
18. Kim, H. J.; Kim, M. R.; So, E. J.; Kim, C. W. (2007). Comparison of proteomes in various human plasma preparations by two-dimensional gel electrophoresis. J Biochem Biophys Methods. 70, 619-625. [PubMed]
19. Kakisaka, T.; Kondo, T.; Okano, T.; Fujii, K.; Honda, K.; Endo, M.; Tsuchida, A.; Aoki, T.; Itoi, T.; Moriyasu, F.; Yamada, T.; Kato, H.; Nishimura, T.; Todo, S.; Hirohashi, S. (2007). Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer. J Chromatogr B Analyt Technol Biomed Life Sci. 852, 257-267. [PubMed]
20. Manabe, T.; Jin, Y.; Tani, O. (2007). Assignment of human plasma polypeptides on a nondenaturing 2-D gel using MALDI-MS and PMF and comparisons with the results of intact protein mapping. Electrophoresis. 28, 843-863. [PubMed]
21. Gundry, R. L.; Fu, Q.; Jelinek, C. A.; Van Eyk, J. E.; Cotter, R. J. (2007). Investigation of an albumin-enriched fraction of human serum and its albuminome. Proteomics Clin Appl. 1, 73-88. [PubMed]
22. Hoffman, S. A.; Joo, W. A.; Echan, L. A.; Speicher, D. W. (2007). Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma. J Chromatogr B Analyt Technol Biomed Life Sci. 849, 43-52. [PubMed]
23. Valentine, S. J.; Plasencia, M. D.; Liu, X.; Krishnan, M.; Naylor, S.; Udseth, H. R.; Smith, R. D.; Clemmer, D. E. (2006). Toward plasma proteome profiling with ion mobility-mass spectrometry. J Proteome Res. 5, 2977-2984. [PubMed]
24. Zhou, M.; Prieto, D. A.; Lucas, D. A.; Chan, K. C.; Issaq, H. J.; Veenstra, T. D.; Conrads, T. P. (2006). Identification of the SELDI ProteinChip human serum retentate by microcapillary liquid chromatography-tandem mass spectrometry. J Proteome Res. 5, 2207-2216. [PubMed]
25. Tanaka, Y.; Akiyama, H.; Kuroda, T.; Jung, G.; Tanahashi, K.; Sugaya, H.; Utsumi, J.; Kawasaki, H.; Hirano, H. (2006). A novel approach and protocol for discovering extremely low-abundance proteins in serum. Proteomics. 6, 4845-4855. [PubMed]
26. Okano, T.; Kondo, T.; Kakisaka, T.; Fujii, K.; Yamada, M.; Kato, H.; Nishimura, T.; Gemma, A.; Kudoh, S.; Hirohashi, S. (2006). Plasma proteomics of lung cancer by a linkage of multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis. Proteomics. 6, 3938-3948. [PubMed]
27. Gong, Y.; Li, X.; Yang, B.; Ying, W.; Li, D.; Zhang, Y.; Dai, S.; Cai, Y.; Wang, J.; He, F.; Qian, X. (2006). Different immunoaffinity fractionation strategies to characterize the human plasma proteome. J Proteome Res. 5, 1379-1387. [PubMed]
28. Zheng, X.; Baker, H.; Hancock, W. S. (2006). Analysis of the low molecular weight serum peptidome using ultrafiltration and a hybrid ion trap-Fourier transform mass spectrometer. J Chromatogr A. 1120, 173-184. [PubMed]
29. States, D. J.; Omenn, G. S.; Blackwell, T. W.; Fermin, D.; Eng, J.; Speicher, D. W.; Hanash, S. M. (2006). Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol. 24, 333-338. [PubMed]
30. Michel, P. E.; Crettaz, D.; Morier, P.; Heller, M.; Gallot, D.; Tissot, J. D.; Reymond, F.; Rossier, J. S. (2006). Proteome analysis of human plasma and amniotic fluid by Off-Gel isoelectric focusing followed by nano-LC-MS/MS. Electrophoresis. 27, 1169-1181. [PubMed]
31. Herosimczyk, A.; Dejeans, N.; Sayd, T.; Ozgo, M.; Skrzypczak, W. F.; Mazur, A. (2006). Plasma proteome analysis: 2D gels and chips. J Physiol Pharmacol. 57 Suppl 7, 81-93. [PubMed]
32. Shen, Y.; Kim, J.; Strittmatter, E. F.; Jacobs, J. M.; Camp, D. G., 2nd; Fang, R.; Tolie, N.; Moore, R. J.; Smith, R. D. (2005). Characterization of the human blood plasma proteome. Proteomics. 5, 4034-4045. [PubMed]
33. Wasinger, V. C.; Locke, V. L.; Raftery, M. J.; Larance, M.; Rothemund, D.; Liew, A.; Bate, I.; Guilhaus, M. (2005). Two-dimensional liquid chromatography/tandem mass spectrometry analysis of Gradiflow fractionated native human plasma. Proteomics. 5, 3397-3401. [PubMed]
34. Omenn, G. S.; States, D. J.; Adamski, M.; Blackwell, T. W.; Menon, R.; Hermjakob, H.; Apweiler, R.; Haab, B. B.; Simpson, R. J.; Eddes, J. S.; Kapp, E. A.; Moritz, R. L.; Chan, D. W.; Rai, A. J.; Admon, A.; Aebersold, R.; Eng, J.; Hancock, W. S.; Hefta, S. A.; Meyer, H.; Paik, Y. K.; Yoo, J. S.; Ping, P.; Pounds, J.; Adkins, J.; Qian, X.; Wang, R.; Wasinger, V.; Wu, C. Y.; Zhao, X.; Zeng, R.; Archakov, A.; Tsugita, A.; Beer, I.; Pandey, A.; Pisano, M.; Andrews, P.; Tammen, H.; Speicher, D. W.; Hanash, S. M. (2005). Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 5, 3226-3245. [PubMed]
35. Tu, C. J.; Dai, J.; Li, S. J.; Sheng, Q. H.; Deng, W. J.; Xia, Q. C.; Zeng, R. (2005). High-sensitivity analysis of human plasma proteome by immobilized isoelectric focusing fractionation coupled to mass spectrometry identification. J Proteome Res. 4, 1265-1273. [PubMed]
36. Moritz, R. L.; Clippingdale, A. B.; Kapp, E. A.; Eddes, J. S.; Ji, H.; Gilbert, S.; Connolly, L. M.; Simpson, R. J. (2005). Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins. Proteomics. 5, 3402-3413. [PubMed]
37. Deutsch, E. W.; Eng, J. K.; Zhang, H.; King, N. L.; Nesvizhskii, A. I.; Lin, B.; Lee, H.; Yi, E. C.; Ossola, R.; Aebersold, R. (2005). Human Plasma PeptideAtlas. Proteomics. 5, 3497-3500. [PubMed]
38. Berhane, B. T.; Zong, C.; Liem, D. A.; Huang, A.; Le, S.; Edmondson, R. D.; Jones, R. C.; Qiao, X.; Whitelegge, J. P.; Ping, P.; Vondriska, T. M. (2005). Cardiovascular-related proteins identified in human plasma by the HUPO Plasma Proteome Project pilot phase. Proteomics. 5, 3520-3530. [PubMed]
39. He, P.; He, H. Z.; Dai, J.; Wang, Y.; Sheng, Q. H.; Zhou, L. P.; Zhang, Z. S.; Sun, Y. L.; Liu, F.; Wang, K.; Zhang, J. S.; Wang, H. X.; Song, Z. M.; Zhang, H. R.; Zeng, R.; Zhao, X. (2005). The human plasma proteome: analysis of Chinese serum using shotgun strategy. Proteomics. 5, 3442-3453. [PubMed]
40. Barnea, E.; Sorkin, R.; Ziv, T.; Beer, I.; Admon, A. (2005). Evaluation of prefractionation methods as a preparatory step for multidimensional based chromatography of serum proteins. Proteomics. 5, 3367-3375. [PubMed]
41. Misek, D. E.; Kuick, R.; Wang, H.; Galchev, V.; Deng, B.; Zhao, R.; Tra, J.; Pisano, M. R.; Amunugama, R.; Allen, D.; Walker, A. K.; Strahler, J. R.; Andrews, P.; Omenn, G. S.; Hanash, S. M. (2005). A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system. Proteomics. 5, 3343-3352. [PubMed]
42. Nedelkov, D.; Kiernan, U. A.; Niederkofler, E. E.; Tubbs, K. A.; Nelson, R. W. (2005). Investigating diversity in human plasma proteins. Proc Natl Acad Sci U S A. 102, 10852-10857. [PubMed]
43. Jin, W. H.; Dai, J.; Li, S. J.; Xia, Q. C.; Zou, H. F.; Zeng, R. (2005). Human plasma proteome analysis by multidimensional chromatography prefractionation and linear ion trap mass spectrometry identification. J Proteome Res. 4, 613-619. [PubMed]
44. Qian, W. J.; Monroe, M. E.; Liu, T.; Jacobs, J. M.; Anderson, G. A.; Shen, Y.; Moore, R. J.; Anderson, D. J.; Zhang, R.; Calvano, S. E.; Lowry, S. F.; Xiao, W.; Moldawer, L. L.; Davis, R. W.; Tompkins, R. G.; Camp, D. G., 2nd; Smith, R. D. (2005). Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach. Mol Cell Proteomics. 4, 700-709. [PubMed]
45. Fujii, K.; Nakano, T.; Kanazawa, M.; Akimoto, S.; Hirano, T.; Kato, H.; Nishimura, T. (2005). Clinical-scale high-throughput human plasma proteome analysis: lung adenocarcinoma. Proteomics. 5, 1150-1159. [PubMed]
46. Qian, W. J.; Jacobs, J. M.; Camp, D. G., 2nd; Monroe, M. E.; Moore, R. J.; Gritsenko, M. A.; Calvano, S. E.; Lowry, S. F.; Xiao, W.; Moldawer, L. L.; Davis, R. W.; Tompkins, R. G.; Smith, R. D. (2005). Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry. Proteomics. 5, 572-584. [PubMed]
47. Chen, J. H.; Chang, Y. W.; Yao, C. W.; Chiueh, T. S.; Huang, S. C.; Chien, K. Y.; Chen, A.; Chang, F. Y.; Wong, C. H.; Chen, Y. J. (2004). Plasma proteome of severe acute respiratory syndrome analyzed by two-dimensional gel electrophoresis and mass spectrometry. Proc Natl Acad Sci U S A. 101, 17039-17044. [PubMed]
48. Anderson, N. L.; Polanski, M.; Pieper, R.; Gatlin, T.; Tirumalai, R. S.; Conrads, T. P.; Veenstra, T. D.; Adkins, J. N.; Pounds, J. G.; Fagan, R.; Lobley, A. (2004). The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol Cell Proteomics. 3, 311-326. [PubMed]
49. Tirumalai, R. S.; Chan, K. C.; Prieto, D. A.; Issaq, H. J.; Conrads, T. P.; Veenstra, T. D. (2003). Characterization of the low molecular weight human serum proteome. Mol Cell Proteomics. 2, 1096-1103. [PubMed]
50. Valentine, S. J.; Plasencia, M. D.; Liu, X.; Krishnan, M.; Naylor, S.; Udseth, H. R.; Smith, R. D.; Clemmer, D. E. (2006). Toward plasma proteome profiling with ion mobility-mass spectrometry. J Proteome Res. 5, 2977-2984. [PubMed]
51. Zhang, Y.; Zhang, Y.; Adachi, J.; Olsen, J. V.; Shi, R.; de Souza, G.; Pasini, E.; Foster, L. J.; Macek, B.; Zougman, A.; Kumar, C.; Wisniewski, J. R.; Jun, W.; Mann, M. (2007). MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes. Nucleic Acids Res. 35, D771-779. [PubMed]
52. Liu, X.; Valentine, S. J.; Plasencia, M. D.; Trimpin, S.; Naylor, S.; Clemmer, D. E. (2007). Mapping the human plasma proteome by SCX-LC-IMS-MS. J Am Soc Mass Spectrom. 18, 1249-1264. [PubMed]
53. Li, S. J.; Peng, M.; Li, H.; Liu, B. S.; Wang, C.; Wu, J. R.; Li, Y. X.; Zeng, R. (2009). Sys-BodyFluid: a systematical database for human body fluid proteome research. Nucleic Acids Res. 37, D907-912. [PubMed]
54. Jeong, S. K.; Lee, E. Y.; Cho, J. Y.; Lee, H. J.; Jeong, A. S.; Cho, S. Y.; Paik, Y. K. (2010). Data management and functional annotation of the Korean reference plasma proteome. Proteomics. 10, 1250-1255. [PubMed]
 

 


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