Review articles Research articles     1. Sung, H. J., Jeon, S. A., Ahn, J. M., Seul, K. J., Kim, J. Y., Lee, J. Y., Yoo, J. S., Lee, S. Y., Kim, H. and Cho, J. Y.  Large-scale isotype-specific quantification of Serum amyloid A 1/2 by multiple reaction monitoring in crude sera. Journal of Proteomics. 2012. 75, 2170-2180. [PubMed] 2. Kuhn, E., Whiteaker, J. R., Mani, D. R., Jackson, A. M., Zhao, L., Pope, M. E., Smith, D., Rivera, K. D., Anderson, N. L., Skates, S. J., Pearson, T. W., Paulovich, A. G. and Carr, S. A.  Inter-laboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Molecular & Cellular Proteomics : MCP. 2011. [PubMed] 3. Ahn, Y. H., Ji, E. S., Shin, P. M., Kim, K. H., Kim, Y. S., Ko, J. H. and Yoo, J. S.  A multiplex lectin-channel monitoring method for human serum glycoproteins by quantitative mass spectrometry. The Analyst. 2012. 137, 691-703. [PubMed] 4. Lee, J. Y., Kim, J. Y., Park, G. W., Cheon, M. H., Kwon, K. H., Ahn, Y. H., Moon, M. H., Lee, H. J., Paik, Y. K. and Yoo, J. S.  Targeted mass spectrometric approach for biomarker discovery and validation with nonglycosylated tryptic peptides from N-linked glycoproteins in human plasma. Molecular & Cellular Proteomics : MCP. 2011. 10, M111.009290. [PubMed] 5. Shi, T., Zhou, J. Y., Gritsenko, M. A., Hossain, M., Camp, D. G., Smith, R. D. and Qian, W. J.  IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomics biomarker discovery. Methods. 2012. 56, 246-253. [PubMed] 6. Tang, H. Y., Beer, L. A., Barnhart, K. T. and Speicher, D. W.  Rapid verification of candidate serological biomarkers using gel-based, label-free multiple reaction monitoring. Journal of Proteome Research. 2011. 10, 4005-4017. [PubMed] 7. Addona, T. A., Shi, X., Keshishian, H., Mani, D. R., Burgess, M., Gillette, M. A., Clauser, K. R., Shen, D., Lewis, G. D., Farrell, L. A., Fifer, M. A., Sabatine, M. S., Gerszten, R. E. and Carr, S. A.  A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. Nature Biotechnology. 2011. 29, 635-643. [PubMed] 8. 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. and Aebersold, R.  A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Molecular & Cellular Proteomics : MCP. 2011. 10, M110.006353. [PubMed] 9. Millioni, R., Tolin, S., Puricelli, L., Sbrignadello, S., Fadini, G. P., Tessari, P. and Arrigoni, G.  High abundance proteins depletion vs low abundance proteins enrichment: comparison of methods to reduce the plasma proteome complexity. PloS One. 2011. 6, e19603. [PubMed] 10. Lee, H. J., Na, K., Kwon, M. S., Park, T., Kim, K. S., Kim, H. and Paik, Y. K.  A new versatile peptide-based size exclusion chromatography platform for global profiling and quantitation of candidate biomarkers in hepatocellular carcinoma specimens. Proteomics. 2011. 11, 1976-1984. [PubMed] 11. Whiteaker, J. R., Zhao, L., Abbatiello, S. E., Burgess, M., Kuhn, E., Lin, C., Pope, M. E., Razavi, M., Anderson, N. L., Pearson, T. W., Carr, S. A. and Paulovich, A. G.  Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry. Molecular & Cellular Proteomics : MCP. 2011. 10, M110.005645. [PubMed] 12. McKay, M. J., Sherman, J., Laver, M. T., Baker, M. S., Clarke, S. J. and Molloy, M. P.  The development of multiple reaction monitoring assays for liver-derived plasma proteins. Proteomics. Clinical Applications. 2007. 1, 1570-1581. [PubMed] 13. Shuford, C. M., Hawkridge, A. M., Burnett, J. C. and Muddiman, D. C.  Utilizing spectral counting to quantitatively characterize tandem removal of abundant proteins (TRAP) in human plasma. Analytical Chemistry. 2010. 82, 10179-10185. [PubMed] 14. Prakash, A., Rezai, T., Krastins, B., Sarracino, D., Athanas, M., Russo, P., Ross, M. M., Zhang, H., Tian, Y., Kulasingam, V., Drabovich, A. P., Smith, C., Batruch, I., Liotta, L., Petricoin, E., Diamandis, E. P., Chan, D. W. and Lopez, M. F.  Platform for establishing interlaboratory reproducibility of selected reaction monitoring-based mass spectrometry peptide assays. Journal of Proteome Research. 2010. 9, 6678-6688. [PubMed] 15. Gundry, R. L., Fu, Q., Jelinek, C. A., Van, E. y. k. and Cotter, R. J.  Investigation of an albumin-enriched fraction of human serum and its albuminome. Proteomics. Clinical Applications. 2007. 1, 73-88. [PubMed] 16. Barton, C., Kay, R. G., Gentzer, W., Vitzthum, F. and Pleasance, S.  Development of high-throughput chemical extraction techniques and quantitative HPLC-MS/MS (SRM) assays for clinically relevant plasma proteins. Journal of Proteome Research. 2010. 9, 333-340. [PubMed] 17. Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J., Mani, D. R., Bunk, D. M., Spiegelman, C. H., Zimmerman, L. J., Ham, A. J., Keshishian, H., Hall, S. C., Allen, S., Blackman, R. K., Borchers, C. H., Buck, C., Cardasis, H. L., Cusack, M. P., Dodder, N. G., Gibson, B. W., Held, J. M., Hiltke, T., Jackson, A., Johansen, E. B., Kinsinger, C. R., Li, J., Mesri, M., Neubert, T. A., Niles, R. K., Pulsipher, T. C., Ransohoff, D., Rodriguez, H., Rudnick, P. A., Smith, D., Tabb, D. L., Tegeler, T. J., Variyath, A. M., Vega-Montoto, L. J., Wahlander, A., Waldemarson, S., Wang, M., Whiteaker, J. R., Zhao, L., Anderson, N. L., Fisher, S. J., Liebler, D. C., Paulovich, A. G., Regnier, F. E., Tempst, P. and Carr, S. A.  Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nature Biotechnology. 2009. 27, 633-641. [PubMed] 18. Kuzyk, M. A., Smith, D., Yang, J., Cross, T. J., Jackson, A. M., Hardie, D. B., Anderson, N. L. and Borchers, C. H.  Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Molecular & Cellular Proteomics : MCP. 2009. 8, 1860-1877. [PubMed] 19. Anderson, N. L., Jackson, A., Smith, D., Hardie, D., Borchers, C. and Pearson, T. W.  SISCAPA peptide enrichment on magnetic beads using an in-line bead trap device. Molecular & Cellular Proteomics : MCP. 2009. 8, 995-1005. [PubMed] 20. Li, S. J., Peng, M., Li, H., Liu, B. S., Wang, C., Wu, J. R., Li, Y. X. and Zeng, R.  Sys-BodyFluid: a systematical database for human body fluid proteome research. Nucleic Acids Research. 2009. 37, D907-12. [PubMed] 21. Schenk, S., Schoenhals, G. J., de, S. and Mann, M.  A high confidence, manually validated human blood plasma protein reference set. BMC Medical Genomics. 2008. 1, 41. [PubMed] 22. Qian, W. J., Kaleta, D. T., Petritis, B. O., Jiang, H., Liu, T., Zhang, X., Mottaz, H. M., Varnum, S. M., Camp, D. G., Huang, L., Fang, X., Zhang, W. W. and Smith, R. D.  Enhanced detection of low abundance human plasma proteins using a tandem IgY12-SuperMix immunoaffinity separation strategy. Molecular & Cellular Proteomics : MCP. 2008. 7, 1963-1973. [PubMed] 23. Zhang, Q., Tang, N., Schepmoes, A. A., Phillips, L. S., Smith, R. D. and Metz, T. O.  Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes. Journal of Proteome Research. 2008. 7, 2025-2032. [PubMed] 24. Sennels, L., Salek, M., Lomas, L., Boschetti, E., Righetti, P. G. and Rappsilber, J.  Proteomic analysis of human blood serum using peptide library beads. Journal of Proteome Research. 2007. 6, 4055-4062. [PubMed] 25. Stahl-Zeng, J., Lange, V., Ossola, R., Eckhardt, K., Krek, W., Aebersold, R. and Domon, B.  High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Molecular & Cellular Proteomics : MCP. 2007. 6, 1809-1817. [PubMed] 26. Kay, R. G., Gregory, B., Grace, P. B. and Pleasance, S.  The application of ultra-performance liquid chromatography/tandem mass spectrometry to the detection and quantitation of apolipoproteins in human serum. Rapid Communications in Mass Spectrometry : RCM. 2007. 21, 2585-2593. [PubMed] 27. Hagglund, P., Matthiesen, R., Elortza, F., Hojrup, P., Roepstorff, P., Jensen, O. N. and Bunkenborg, J.  An enzymatic deglycosylation scheme enabling identification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins. Journal of Proteome Research. 2007. 6, 3021-3031. [PubMed] 28. Zhou, Y., Aebersold, R. and Zhang, H.  Isolation of N-linked glycopeptides from plasma. Analytical Chemistry. 2007. 79, 5826-5837. [PubMed] 29. Liu, X., Valentine, S. J., Plasencia, M. D., Trimpin, S., Naylor, S. and Clemmer, D. E.  Mapping the human plasma proteome by SCX-LC-IMS-MS. Journal of the American Society For Mass Spectrometry. 2007. 18, 1249-1264. [PubMed] 30. Whiteaker, J. R., Zhang, H., Eng, J. K., Fang, R., Piening, B. D., Feng, L. C., Lorentzen, T. D., Schoenherr, R. M., Keane, J. F., Holzman, T., Fitzgibbon, M., Lin, C., Zhang, H., Cooke, K., Liu, T., Camp, D. G., Anderson, L., Watts, J., Smith, R. D., McIntosh, M. W. and Paulovich, A. G.  Head-to-head comparison of serum fractionation techniques. Journal of Proteome Research. 2007. 6, 828-836. [PubMed] 31. Herosimczyk, A., Dejeans, N., Sayd, T., Ozgo, M., Skrzypczak, W. F. and Mazur, A.  Plasma proteome analysis: 2D gels and chips. Journal of Physiology and Pharmacology : An Official Journal of the Polish Physiological Society. 2006. 57 Suppl 7, 81-93. [PubMed] 32. Zhang, Y., Zhang, Y., Adachi, J., Olsen, J. V., Shi, R., de, S., Pasini, E., Foster, L. J., Macek, B., Zougman, A., Kumar, C., Wisniewski, J. R., Jun, W. and Mann, M.  MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes. Nucleic Acids Research. 2007. 35, D771-9. [PubMed] 33. Valentine, S. J., Plasencia, M. D., Liu, X., Krishnan, M., Naylor, S., Udseth, H. R., Smith, R. D. and Clemmer, D. E.  Toward plasma proteome profiling with ion mobility-mass spectrometry. Journal of Proteome Research. 2006. 5, 2977-2984. [PubMed] 34. Zhang, H., Liu, A. Y., Loriaux, P., Wollscheid, B., Zhou, Y., Watts, J. D. and Aebersold, R.  Mass spectrometric detection of tissue proteins in plasma. Molecular & Cellular Proteomics : MCP. 2007. 6, 64-71. [PubMed] 35. Zhou, M., Prieto, D. A., Lucas, D. A., Chan, K. C., Issaq, H. J., Veenstra, T. D. and Conrads, T. P.  Identification of the SELDI ProteinChip human serum retentate by microcapillary liquid chromatography-tandem mass spectrometry. Journal of Proteome Research. 2006. 5, 2207-2216. [PubMed] 36. Tanaka, Y., Akiyama, H., Kuroda, T., Jung, G., Tanahashi, K., Sugaya, H., Utsumi, J., Kawasaki, H. and Hirano, H.  A novel approach and protocol for discovering extremely low-abundance proteins in serum. Proteomics. 2006. 6, 4845-4855. [PubMed] 37. Okano, T., Kondo, T., Kakisaka, T., Fujii, K., Yamada, M., Kato, H., Nishimura, T., Gemma, A., Kudoh, S. and Hirohashi, S.  Plasma proteomics of lung cancer by a linkage of multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis. Proteomics. 2006. 6, 3938-3948. [PubMed] 38. Gong, Y., Li, X., Yang, B., Ying, W., Li, D., Zhang, Y., Dai, S., Cai, Y., Wang, J., He, F. and Qian, X.  Different immunoaffinity fractionation strategies to characterize the human plasma proteome. Journal of Proteome Research. 2006. 5, 1379-1387. [PubMed] 39. Liu, T., Qian, W. J., Gritsenko, M. A., Xiao, W., Moldawer, L. L., Kaushal, A., Monroe, M. E., Varnum, S. M., Moore, R. J., Purvine, S. O., Maier, R. V., Davis, R. W., Tompkins, R. G., Camp, D. G. and Smith, R. D.  High dynamic range characterization of the trauma patient plasma proteome. Molecular & Cellular Proteomics : MCP. 2006. 5, 1899-1913. [PubMed] 40. Zheng, X., Baker, H. and Hancock, W. S.  Analysis of the low molecular weight serum peptidome using ultrafiltration and a hybrid ion trap-Fourier transform mass spectrometer. Journal of Chromatography. A. 2006. 1120, 173-184. [PubMed] 41. States, D. J., Omenn, G. S., Blackwell, T. W., Fermin, D., Eng, J., Speicher, D. W. and Hanash, S. M.  Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nature Biotechnology. 2006. 24, 333-338. [PubMed] 42. Liu, T., Qian, W. J., Gritsenko, M. A., Camp, D. G., Monroe, M. E., Moore, R. J. and Smith, R. D.  Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. Journal of Proteome Research. 2005. 4, 2070-2080. [PubMed] 43. Wasinger, V. C., Locke, V. L., Raftery, M. J., Larance, M., Rothemund, D., Liew, A., Bate, I. and Guilhaus, M.  Two-dimensional liquid chromatography/tandem mass spectrometry analysis of Gradiflow fractionated native human plasma. Proteomics. 2005. 5, 3397-3401. [PubMed] 44. 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. and Hanash, S. M.  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. 2005. 5, 3226-3245. [PubMed] 45. Tu, C. J., Dai, J., Li, S. J., Sheng, Q. H., Deng, W. J., Xia, Q. C. and Zeng, R.  High-sensitivity analysis of human plasma proteome by immobilized isoelectric focusing fractionation coupled to mass spectrometry identification. Journal of Proteome Research. 2005. 4, 1265-1273. [PubMed] 46. Moritz, R. L., Clippingdale, A. B., Kapp, E. A., Eddes, J. S., Ji, H., Gilbert, S., Connolly, L. M. and Simpson, R. J.  Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins. Proteomics. 2005. 5, 3402-3413. [PubMed] 47. Deutsch, E. W., Eng, J. K., Zhang, H., King, N. L., Nesvizhskii, A. I., Lin, B., Lee, H., Yi, E. C., Ossola, R. and Aebersold, R.  Human Plasma PeptideAtlas. Proteomics. 2005. 5, 3497-3500. [PubMed] 48. 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. and Vondriska, T. M.  Cardiovascular-related proteins identified in human plasma by the HUPO Plasma Proteome Project pilot phase. Proteomics. 2005. 5, 3520-3530. [PubMed] 49. 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. and Zhao, X.  The human plasma proteome: analysis of Chinese serum using shotgun strategy. Proteomics. 2005. 5, 3442-3453. [PubMed] 50. Barnea, E., Sorkin, R., Ziv, T., Beer, I. and Admon, A.  Evaluation of prefractionation methods as a preparatory step for multidimensional based chromatography of serum proteins. Proteomics. 2005. 5, 3367-3375. [PubMed] 51. 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. and Hanash, S. M.  A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system. Proteomics. 2005. 5, 3343-3352. [PubMed] 52. Nedelkov, D., Kiernan, U. A., Niederkofler, E. E., Tubbs, K. A. and Nelson, R. W.  Investigating diversity in human plasma proteins. Proceedings of the National Academy of Sciences of the United States of America. 2005. 102, 10852-10857. [PubMed] 53. Haab, B. B., Geierstanger, B. H., Michailidis, G., Vitzthum, F., Forrester, S., Okon, R., Saviranta, P., Brinker, A., Sorette, M., Perlee, L., Suresh, S., Drwal, G., Adkins, J. N. and Omenn, G. S.  Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: systematic variation between sample types and calibration of mass spectrometry data. Proteomics. 2005. 5, 3278-3291. [PubMed] 54. Jin, W. H., Dai, J., Li, S. J., Xia, Q. C., Zou, H. F. and Zeng, R.  Human plasma proteome analysis by multidimensional chromatography prefractionation and linear ion trap mass spectrometry identification. Journal of Proteome Research. 2005. 4, 613-619. [PubMed] 55. 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. and Smith, R. D.  Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach. Molecular & Cellular Proteomics : MCP. 2005. 4, 700-709. [PubMed] 56. Anderson, N. L., Anderson, N. G., Haines, L. R., Hardie, D. B., Olafson, R. W. and Pearson, T. W.  Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). Journal of Proteome Research. 2004. 3, 235-244. [PubMed] 57. 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. and Lobley, A.  The human plasma proteome: a nonredundant list developed by combination of four separate sources. Molecular & Cellular Proteomics : MCP. 2004. 3, 311-326. [PubMed] 58. Tirumalai, R. S., Chan, K. C., Prieto, D. A., Issaq, H. J., Conrads, T. P. and Veenstra, T. D.  Characterization of the low molecular weight human serum proteome. Molecular & Cellular Proteomics : MCP. 2003. 2, 1096-1103. [PubMed] 59. Pieper, R., Gatlin, C. L., Makusky, A. J., Russo, P. S., Schatz, C. R., Miller, S. S., Su, Q., McGrath, A. M., Estock, M. A., Parmar, P. P., Zhao, M., Huang, S. T., Zhou, J., Wang, F., Esquer-Blasco, R., Anderson, N. L., Taylor, J. and Steiner, S.  The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics. 2003. 3, 1345-1364. [PubMed] 60. Pieper, R., Su, Q., Gatlin, C. L., Huang, S. T., Anderson, N. L. and Steiner, S.  Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome. Proteomics. 2003. 3, 422-432. [PubMed]