Protein and peptide fractionation, enrichment and depletion: Tools for the complex proteome

Proteomics

Volumn 11, Issue 4, 2011, Pages 513-534

  Ly, Linda ^a   Wasinger, Valerie C ^b  

^a UNIVERSITY OF SYDNEY   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

Chromatography; Electrophoresis; Fractionation; Protein; Proteome; Technology

Indexed keywords

HISTONE H1; HISTONE H2A; HISTONE H2B; HISTONE H3; HISTONE H4; PROTEOME;

AFFINITY CHROMATOGRAPHY; CAPILLARY ELECTROPHORESIS; CAPILLARY ZONE ELECTROPHORESIS; ELECTROSPRAY; GEL PERMEATION CHROMATOGRAPHY; HUMAN; ION EXCHANGE CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY MASS SPECTROMETRY; MASS SPECTROMETRY; NONHUMAN; PEPTIDE ANALYSIS; PH; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; REVERSED PHASE LIQUID CHROMATOGRAPHY; REVIEW; ZONE ELECTROPHORESIS;

CHEMICAL FRACTIONATION; CHEMISTRY TECHNIQUES, ANALYTICAL; CHROMATOGRAPHY, LIQUID; ELECTROPHORESIS; PROTEINS; PROTEOMICS;

EID: 79551474552     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000394     Document Type: Review

References (213)

1. Wasinger, V. C., Cordwell, S. J., Cerpa-Poljak, A., Yan, J. X. et al., Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 1995, 16, 1090-1094.
2. Wilkins, M. R., Pasquali, C., Appel, R. D., Ou, K. et al., From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (NY) 1996, 14, 61-65.
3. Mann, M., Jensen, O. N., Proteomic analysis of post-translational modifications. Nat. Biotechnol. 2003, 21, 255-261.
4. Patterson, S. D., Aebersold, R. H., Proteomics: the first decade and beyond. Nat. Genet. 2003, 33, 311-323.
5. Wasinger, V. C., Corthals, G. L., Proteomic tools for biomedicine. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2002, 771, 33-48.
6. O'Farrell, P. H., High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 1975, 250, 4007-4021.
7. Wang, J., Gu, Y., Wang, L., Hang, X. et al., HUPO BPP pilot study: a proteomics analysis of the mouse brain of different developmental stages. Proteomics 2007, 7, 4008-4015.
8. McNicoll, F., Drummelsmith, J., Muller, M., Madore, E. et al., A combined proteomic and transcriptomic approach to the study of stage differentiation in Leishmania infantum. Proteomics 2006, 6, 3567-3581.
9. Peng, J., Gygi, S. P., Proteomics: the move to mixtures. J. Mass Spectrom. 2001, 36, 1083-1091.
10. Rabilloud, T., Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2002, 2, 3-10.
11. Corthals, G. L., Wasinger, V. C., Hochstrasser, D. F., Sanchez, J. C., The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 2000, 21, 1104-1115.
12. Anderson, N. L., Anderson, N. G., The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell Proteomics 2002, 1, 845-867.
13. Qian, W. J., Jacobs, J. M., Liu, T., Camp, D. G., 2nd., Smith, R. D., Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol. Cell Proteomics 2006, 5, 1727-1744.
14. Baggerman, G., Vierstraete, E., De Loof, A., Schoofs, L., Gel-based versus gel-free proteomics: a review. Comb. Chem. High Throughput Screen 2005, 8, 669-677.
15. Gorg, A., Weiss, W., Dunn, M. J., Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004, 4, 3665-3685.
16. Miller, I., Crawford, J., Gianazza, E., Protein stains for proteomic applications: which, when, why? Proteomics 2006, 6, 5385-5408.
17. Baharvand, H., Fathi, A., van Hoof, D., Salekdeh, G. H., Concise review: trends in stem cell proteomics. Stem Cells 2007, 25, 1888-1903.
18. Neuhoff, V., Arold, N., Taube, D., Ehrhardt, W., Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250. Electrophoresis 1988, 9, 255-262.
19. Blum, H., Beier, H., Gross, H. J., Improved silver staining of plant proteins, RNA and DNA in polyacrylamide gels. Electrophoresis 1987, 8, 93-99.
20. Patton, W. F., Detection technologies in proteome analysis. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2002, 771, 3-31.
21. Mackintosh, J. A., Choi, H. Y., Bae, S. H., Veal, D. A. et al., A fluorescent natural product for ultra sensitive detection of proteins in one-dimensional and two-dimensional gel electrophoresis. Proteomics 2003, 3, 2273-2288.
22. Marouga, R., David, S., Hawkins, E., The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal. Bioanal. Chem. 2005, 382, 669-678.
23. Shaw, J., Rowlinson, R., Nickson, J., Stone, T. et al., Evaluation of saturation labelling two-dimensional difference gel electrophoresis fluorescent dyes. Proteomics 2003, 3, 1181-1195.
24. Tonge, R., Shaw, J., Middleton, B., Rowlinson, R. et al., Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 2001, 1, 377-396.
25. Smith, R. D., Trends in mass spectrometry instrumentation for proteomics. Trends Biotechnol. 2002, 20, S3-S7.
26. Shen, Y., Smith, R. D., Unger, K. K., Kumar, D., Lubda, D., Ultrahigh-throughput proteomics using fast RPLC separations with ESI-MS/MS. Anal. Chem. 2005, 77, 6692-6701.
27. Shen, Y., Jacobs, J. M., Camp, D. G., 2nd., Fang, R. et al., Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal. Chem. 2004, 76, 1134-1144.
28. Issaq, H. J., Conrads, T. P., Janini, G. M., Veenstra, T. D., Methods for fractionation, separation and profiling of proteins and peptides. Electrophoresis 2002, 23, 3048-3061.
29. Omenn, G. S., States, D. J., Adamski, M., Blackwell, T. W. et al., 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.
30. Barnea, E., Sorkin, R., Ziv, T., Beer, I., Admon, A., Evaluation of prefractionation methods as a preparatory step for multidimensional based chromatography of serum proteins. Proteomics 2005, 5, 3367-3375.
31. Kim, J. Y., Lee, J. H., Park, G. W., Cho, K. et al., Utility of electrophoretically derived protein mass estimates as additional constraints in proteome analysis of human serum based on MS/MS analysis. Proteomics 2005, 5, 3376-3385.
32. Tang, H. Y., Ali-Khan, N., Echan, L. A., Levenkova, N. et al., A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes. Proteomics 2005, 5, 3329-3342.
33. Lescuyer, P., Hochstrasser, D. F., Sanchez, J. C., Comprehensive proteome analysis by chromatographic protein prefractionation. Electrophoresis 2004, 25, 1125-1135.
34. Liu, H., Lin, D., Yates, J. R., 3rd., Multidimensional separations for protein/peptide analysis in the post-genomic era. Biotechniques 2002, 32, 898, 900, 902 passim.
35. Wang, Y., Zhang, J., Gu, X., Zhang, X. M., Protein identification assisted by the prediction of retention time in liquid chromatography/tandem mass spectrometry. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2005, 826, 122-128.
36. Krokhin, O. V., Ying, S., Cortens, J. P., Ghosh, D. et al., Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS. Anal. Chem. 2006, 78, 6265-6269.
37. Eeltink, S., Dolman, S., Swart, R., Ursem, M., Schoenmakers, P. J., Optimizing the peak capacity per unit time in one-dimensional and off-line two-dimensional liquid chromatography for the separation of complex peptide samples. J. Chromatogr. A 2009, 1216, 7368-7374.
38. Ebert, M. P., Niemeyer, D., Deininger, S. O., Wex, T. et al., Identification and confirmation of increased fibrinopeptide a serum protein levels in gastric cancer sera by magnet bead assisted MALDI-TOF mass spectrometry. J. Proteome Res. 2006, 5, 2152-2158.
39. Yuan, X., Desiderio, D. M., Proteomics analysis of prefractionated human lumbar cerebrospinal fluid. Proteomics 2005, 5, 541-550.
40. Martosella, J., Zolotarjova, N., Liu, H., Nicol, G., Boyes, B. E., Reversed-phase high-performance liquid chromatographic prefractionation of immunodepleted human serum proteins to enhance mass spectrometry identification of lower-abundant proteins. J. Proteome Res. 2005, 4, 1522-1537.
41. Lam, Y. W., Mobley, J. A., Evans, J. E., Carmody, J. F., Ho, S. M., Mass profiling-directed isolation and identification of a stage-specific serologic protein biomarker of advanced prostate cancer. Proteomics 2005, 5, 2927-2938.
42. Cellar, N. A., Karnoup, A. S., Albers, D. R., Langhorst, M. L., Young, S. A., Immunodepletion of high abundance proteins coupled on-line with reversed-phase liquid chromatography: a two-dimensional LC sample enrichment and fractionation technique for mammalian proteomics. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2009, 877, 79-85.
43. Su, X., Jacob, N. K., Amunugama, R., Lucas, D. M. et al., Liquid chromatography mass spectrometry profiling of histones. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007, 850, 440-454.
44. Horvatovich, P., Hoekman, B., Govorukhina, N., Bischoff, R., Multidimensional chromatography coupled to mass spectrometry in analysing complex proteomics samples. J. Sep. Sci. 2010, 33, 1421-1437.
45. Pavlou, M. P., Kulasingam, V., Sauter, E. R., Kliethermes, B., Diamandis, E. P., Nipple aspirate fluid proteome of healthy females and patients with breast cancer. Clin. Chem. 2010, 56, 848-855.
46. Fuller, B. F., Ottens, A. K., Separation of the neuroproteome by ion exchange chromatography. Methods Mol. Biol. 2009, 566, 193-200.
47. Rocchiccioli, S., Citti, L., Boccardi, C., Ucciferri, N. et al., A gel-free approach in vascular smooth muscle cell proteome: perspectives for a better insight into activation. Proteome Sci. 2010, 8, 15.
48. Liu, N., Paulus, A., Enriching basic and acidic rat brain proteins with ion exchange mini spin columns before two-dimensional gel electrophoresis. Methods Mol. Biol. 2008, 424, 157-166.
49. Faca, V., Pitteri, S. J., Newcomb, L., Glukhova, V. et al., Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J. Proteome Res. 2007, 6, 3558-3565.
50. Pepaj, M., Wilson, S. R., Novotna, K., Lundanes, E., Greibrokk, T., Two-dimensional capillary liquid chromatography: pH gradient ion exchange and reversed phase chromatography for rapid separation of proteins. J. Chromatogr. A 2006, 1120, 132-141.
51. Gao, M., Deng, C., Yu, W., Zhang, Y. et al., Large scale depletion of the high-abundance proteins and analysis of middle- and low-abundance proteins in human liver proteome by multidimensional liquid chromatography. Proteomics 2008, 8, 939-947.
52. Shin, J. H., Krapfenbauer, K., Lubec, G., Column chromatographic prefractionation leads to the detection of 543 different gene products in human fetal brain. Electrophoresis 2005, 26, 2759-2778.
53. Thongboonkerd, V., Semangoen, T., Chutipongtanate, S., Enrichment of the basic/cationic urinary proteome using ion exchange chromatography and batch adsorption. J. Proteome Res. 2007, 6, 1209-1214.
54. Krapfenbauer, K., Berger, M., Friedlein, A., Lubec, G., Fountoulakis, M., Changes in the levels of low-abundance brain proteins induced by kainic acid. Eur. J. Biochem. 2001, 268, 3532-3537.
55. Righetti, P. G., Castagna, A., Herbert, B., Reymond, F., Rossier, J. S., Prefractionation techniques in proteome analysis. Proteomics 2003, 3, 1397-1407.
56. Shan, L., Anderson, D. J., Gradient chromatofocusing versatile pH gradient separation of proteins in ion-exchange HPLC: characterization studies. Anal. Chem. 2002, 74, 5641-5649.
57. Shan, L., Anderson, D. J., Effect of buffer concentration on gradient chromatofocusing performance separating proteins on a high-performance DEAE column. J. Chromatogr. A 2001, 909, 191-205.
58. Ahamed, T., Nfor, B. K., Verhaert, P. D., van Dedem, G. W. et al., pH-gradient ion-exchange chromatography: an analytical tool for design and optimization of protein separations. J. Chromatogr. A 2007, 1164, 181-188.
59. Ahamed, T., Chilamkurthi, S., Nfor, B. K., Verhaert, P. D. et al., Selection of pH-related parameters in ion-exchange chromatography using pH-gradient operations. J. Chromatogr. A 2008, 1194, 22-29.
60. Pabst, T. M., Antos, D., Carta, G., Ramasubramanyan, N., Hunter, A. K., Protein separations with induced pH gradients using cation-exchange chromatographic columns containing weak acid groups. J. Chromatogr. A 2008, 1181, 83-94.
61. Liu, Y., Anderson, D. J., Gradient chromatofocusing high-performance liquid chromatography. I. Practical aspects. J. Chromatogr. A 1997, 762, 207-217.
62. Kim, H., Lubman, D. M., Micro-proteome analysis using micro-chromatofocusing in intact protein separations. J. Chromatogr. A 2008, 1194, 3-10.
63. Ning, Z. B., Li, Q. R., Dai, J., Li, R. X. et al., Fractionation of complex protein mixture by virtual three-dimensional liquid chromatography based on combined pH and salt steps. J. Proteome Res. 2008, 7, 4525-4537.
64. Fortis, F., Guerrier, L., Girot, P., Fasoli, E. et al., A pI-based protein fractionation method using solid-state buffers. J. Proteomics 2008, 71, 379-389.
65. Restuccia, U., Boschetti, E., Fasoli, E., Fortis, F. et al., pI-based fractionation of serum proteomes versus anion exchange after enhancement of low-abundance proteins by means of peptide libraries. J. Proteomics 2009, 72, 1061-1070.
66. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E. et al., Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 1999, 17, 676-682.
67. Wolters, D. A., Washburn, M. P., Yates, J. R., 3rd., An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 2001, 73, 5683-5690.
68. Washburn, M. P., Wolters, D., Yates, J. R., 3rd., Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19, 242-247.
69. Durr, E., Yu, J., Krasinska, K. M., Carver, L. A. et al., Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat. Biotechnol. 2004, 22, 985-992.
70. Chen, E. I., Hewel, J., Felding-Habermann, B., Yates, J. R., 3rd, Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT). Mol. Cell Proteomics 2006, 5, 53-56.
71. Mitulovic, G., Mechtler, K., HPLC techniques for proteomics analysis - a short overview of latest developments. Brief Funct. Genomic Proteomic 2006, 5, 249-260.
72. Natera, S. H., Ford, K. L., Cassin, A. M., Patterson, J. H. et al., Analysis of the Oryza sativa plasma membrane proteome using combined protein and peptide fractionation approaches in conjunction with mass spectrometry. J. Proteome Res. 2008, 7, 1159-1187.
73. Pan, S., Shi, M., Jin, J., Albin, R. L. et al., Proteomics identification of proteins in human cortex using multidimensional separations and MALDI tandem mass spectrometer. Mol. Cell Proteomics 2007, 6, 1818-1823.
74. Jacobs, J. M., Mottaz, H. M., Yu, L. R., Anderson, D. J. et al., Multidimensional proteome analysis of human mammary epithelial cells. J. Proteome Res. 2004, 3, 68-75.
75. Wagner, Y., Sickmann, A., Meyer, H. E., Daum, G., Multidimensional nano-HPLC for analysis of protein complexes. J. Am. Soc. Mass Spectrom. 2003, 14, 1003-1011.
76. Nagele, E., Vollmer, M., Horth, P., Two-dimensional nano-liquid chromatography-mass spectrometry system for applications in proteomics. J. Chromatogr. A 2003, 1009, 197-205.
77. Mitulovic, G., Stingl, C., Smoluch, M., Swart, R. et al., Automated, on-line two-dimensional nano liquid chromatography tandem mass spectrometry for rapid analysis of complex protein digests. Proteomics 2004, 4, 2545-2557.
78. Zhou, H., Dai, J., Sheng, Q. H., Li, R. X. et al., A fully automated 2-D LC-MS method utilizing online continuous pH and RP gradients for global proteome analysis. Electrophoresis 2007, 28, 4311-4319.
79. Lewandrowski, U., Zahedi, R. P., Moebius, J., Walter, U., Sickmann, A., Enhanced N-glycosylation site analysis of sialoglycopeptides by strong cation exchange prefractionation applied to platelet plasma membranes. Mol. Cell Proteomics 2007, 6, 1933-1941.
80. Taouatas, N., Altelaar, A. F., Drugan, M. M., Helbig, A. O. et al., Strong cation exchange-based fractionation of Lys-N-generated peptides facilitates the targeted analysis of post-translational modifications. Mol. Cell Proteomics 2009, 8, 190-200.
81. Voet, D., Voet, J. G., Pratt, C. W., Fundamentals of Biochemistry, Wiley, New York 1999.
82. Irvine, G. B., Size-exclusion high-performance liquid chromatography of peptides: a review. Anal. Chim. Acta 1997, 352, 387-397.
83. Simpson, D. C., Ahn, S., Pasa-Tolic, L., Bogdanov, B. et al., Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling. Electrophoresis 2006, 27, 2722-2733.
84. Hou, W., Ethier, M., Smith, J. C., Sheng, Y., Figeys, D., Multiplexed proteomic reactor for the processing of proteomic samples. Anal. Chem. 2007, 79, 39-44.
85. Moore, A. W., Jr., Jorgenson, J. W., Comprehensive three-dimensional separation of peptides using size exclusion chromatography/reversed phase liquid chromatography/optically gated capillary zone electrophoresis. Anal. Chem. 1995, 67, 3456-3463.
86. Zhang, K., McKinlay, C., Hocart, C. H., Djordjevic, M. A., The Medicago truncatula small protein proteome and peptidome. J. Proteome Res. 2006, 5, 3355-3367.
87. Li, S. S., Giometti, C. S., A combinatorial approach to studying protein complex composition by employing size-exclusion chromatography and proteome analysis. J. Sep. Sci. 2007, 30, 1549-1555.
88. Hu, L., Boos, K. S., Ye, M., Wu, R., Zou, H., Selective on-line serum peptide extraction and multidimensional separation by coupling a restricted-access material-based capillary trap column with nanoliquid chromatography-tandem mass spectrometry. J. Chromatogr. A 2009, 1216, 5377-5384.
89. Gong, Y., Li, X., Yang, B., Ying, W. et al., Different immunoaffinity fractionation strategies to characterize the human plasma proteome. J. Proteome Res. 2006, 5, 1379-1387.
90. Thingholm, T. E., Larsen, M. R., Ingrell, C. R., Kassem, M., Jensen, O. N., TiO(2)-based phosphoproteomic analysis of the plasma membrane and the effects of phosphatase inhibitor treatment. J. Proteome Res. 2008, 7, 3304-3313.
91. Xie, X., Feng, S., Vuong, H., Liu, Y. et al., A comparative phosphoproteomic analysis of a human tumor metastasis model using a label-free quantitative approach. Electrophoresis 2010, 31, 1842-1852.
92. Lemeer, S., Pinkse, M. W., Mohammed, S., van Breukelen, B. et al., Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo. J. Proteome Res. 2008, 7, 1555-1564.
93. Pinkse, M. W., Uitto, P. M., Hilhorst, M. J., Ooms, B., Heck, A. J., Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal. Chem. 2004, 76, 3935-3943.
94. Gauci, S., van Breukelen, B., Lemeer, S. M., Krijgsveld, J., Heck, A. J., A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing. Proteomics 2008, 8, 4898-4906.
95. Bahl, J. M., Jensen, S. S., Larsen, M. R., Heegaard, N. H., Characterization of the human cerebrospinal fluid phosphoproteome by titanium dioxide affinity chromatography and mass spectrometry. Anal. Chem. 2008, 80, 6308-6316.
96. 2 enrichment in combination with MALDI TOF/TOF MS. Proteomics 2008, 8, 4577-4592.
97. Jensen, S. S., Larsen, M. R., Evaluation of the impact of some experimental procedures on different phosphopeptide enrichment techniques. Rapid Commun. Mass Spectrom. 2007, 21, 3635-3645.
98. Larsen, M. R., Thingholm, T. E., Jensen, O. N., Roepstorff, P., Jorgensen, T. J., Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell Proteomics 2005, 4, 873-886.
99. Thingholm, T. E., Jorgensen, T. J., Jensen, O. N., Larsen, M. R., Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat. Protoc. 2006, 1, 1929-1935.
100. Feng, S., Ye, M., Zhou, H., Jiang, X.et al., Immobilized zirconium ion affinity chromatography for specific enrichment of phosphopeptides in phosphoproteome analysis. Mol. Cell Proteomics 2007, 6, 1656-1665.
101. Cantin, G. T., Yi, W., Lu, B., Park, S. K. et al., Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. J. Proteome Res. 2008, 7, 1346-1351.
102. Morales, M. A., Watanabe, R., Laurent, C., Lenormand, P. et al., Phosphoproteomic analysis of Leishmania donovani pro- and amastigote stages. Proteomics 2008, 8, 350-363.
103. Chiou, S. H., Huang, C. H., Lee, I. L., Wang, Y. T. et al., Identification of in vivo phosphorylation sites of lens proteins from porcine eye lenses by a gel-free phosphoproteomics approach. Mol. Vision 2010, 16, 294-302.
104. Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J. et al., Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 2002, 20, 301-305.
105. Karlsson, G., Winge, S., Separation of latent, prelatent, and native forms of human antithrombin by heparin affinity high-performance liquid chromatography. Protein Expr. Purif. 2004, 33, 339-345.
106. Farooqui, A. A., Purification of enzymes by heparin-sepharose affinity chromatography. J. Chromatogr. 1980, 184, 335-345.
107. Farooqui, A. A., Yang, H. C., Horrocks, L. A., Purification of lipases, phospholipases and kinases by heparin-sepharose chromatography. J. Chromatogr. A 1994, 673, 149-158.
108. Shefcheck, K., Yao, X., Fenselau, C., Fractionation of cytosolic proteins on an immobilized heparin column. Anal. Chem. 2003, 75, 1691-1698.
109. Lei, T., He, Q. Y., Wang, Y. L., Si, L. S., Chiu, J. F., Heparin chromatography to deplete high-abundance proteins for serum proteomics. Clin. Chim. Acta 2008, 388, 173-178.
110. Staby, A., Sand, M. B., Hansen, R. G., Jacobsen, J. H. et al., Comparison of chromatographic ion-exchange resins. IV. Strong and weak cation-exchange resins and heparin resins. J. Chromatogr. A 2005, 1069, 65-77.
111. Dayarathna, M. K., Hancock, W. S., Hincapie, M., A two-step fractionation approach for plasma proteomics using immunodepletion of abundant proteins and multi-lectin affinity chromatography: application to the analysis of obesity, diabetes, and hypertension diseases. J. Sep. Sci. 2008, 31, 1156-1166.
112. Zhao, J., Simeone, D. M., Heidt, D., Anderson, M. A., Lubman, D. M., Comparative serum glycoproteomics using lectin selected sialic acid glycoproteins with mass spectrometric analysis: application to pancreatic cancer serum. J. Proteome Res. 2006, 5, 1792-1802.
113. McDonald, C. A., Yang, J. Y., Marathe, V., Yen, T. Y., Macher, B. A., Combining results from lectin affinity chromatography and glycocapture approaches substantially improves the coverage of the glycoproteome. Mol. Cell Proteomics 2009, 8, 287-301.
114. Geyer, H., Geyer, R., Strategies for analysis of glycoprotein glycosylation. Biochim. Biophys. Acta 2006, 1764, 1853-1869.
115. Lewis, U. J., Singh, R. N., Lewis, L. J., Seavey, B. K., Sinha, Y. N., Glycosylated ovine prolactin. Proc. Natl. Acad. Sci. USA 1984, 81, 385-389.
116. Elia, G., Biotinylation reagents for the study of cell surface proteins. Proteomics 2008, 8, 4012-4024.
117. Ge, Y., Rikihisa, Y., Identification of novel surface proteins of Anaplasma phagocytophilum by affinity purification and proteomics. J. Bacteriol. 2007, 189, 7819-7828.
118. Wu, J., Liu, W., Sousa, E., Qiu, Y. et al., Proteomic identification of endothelial proteins isolated in situ from atherosclerotic aorta via systemic perfusion. J. Proteome Res. 2007, 6, 4728-4736.
119. Kischel, P., Guillonneau, F., Dumont, B., Bellahcene, A. et al., Cell membrane proteomic analysis identifies proteins differentially expressed in osteotropic human breast cancer cells. Neoplasia 2008, 10, 1014-1020.
120. Rybak, J. N., Ettorre, A., Kaissling, B., Giavazzi, R. et al., In vivo protein biotinylation for identification of organ-specific antigens accessible from the vasculature. Nat. Methods 2005, 2, 291-298.
121. Cordwell, S. J., Technologies for bacterial surface proteomics. Curr. Opin. Microbiol. 2006, 9, 320-329.
122. Green, N. M., Toms, E. J., The properties of subunits of avidin coupled to sepharose. Biochem. J. 1973, 133, 687-700.
123. Bayer, E. A., Wilchek, M., Application of avidin-biotin technology to affinity-based separations. J. Chromatogr. 1990, 510, 3-11.
124. Polaskova, V., Kapur, A., Khan, A., Molloy, M. P., Baker, M. S., High-abundance protein depletion: comparison of methods for human plasma biomarker discovery. Electrophoresis 2010, 31, 471-482.
125. Lai, X., Bacallao, R. L., Blazer-Yost, B. L., Hong, D. et al., Characterization of the renal cyst fluid proteome in autosomal dominant polycystic kidney disease (ADPKD) patients. Proteomics Clin. Appl. 2008, 2, 1140-1152.
126. Huang, L., Harvie, G., Feitelson, J. S., Gramatikoff, K. et al., Immunoaffinity separation of plasma proteins by IgY microbeads: meeting the needs of proteomic sample preparation and analysis. Proteomics 2005, 5, 3314-3328.
127. Linke, T., Doraiswamy, S., Harrison, E. H., Rat plasma proteomics: effects of abundant protein depletion on proteomic analysis. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007, 849, 273-281.
128. Ogata, Y., Charlesworth, M. C., Muddiman, D. C., Evaluation of protein depletion methods for the analysis of total-, phospho- and glycoproteins in lumbar cerebrospinal fluid. J. Proteome Res. 2005, 4, 837-845.
129. Seam, N., Gonzales, D. A., Kern, S. J., Hortin, G. L. et al., Quality control of serum albumin depletion for proteomic analysis. Clin. Chem. 2007, 53, 1915-1920.
130. Freeman, W. M., Lull, M. E., Guilford, M. T., Vrana, K. E., Depletion of abundant proteins from non-human primate serum for biomarker studies. Proteomics 2006, 6, 3109-3113.
131. Tyan, Y. C., Guo, H. R., Liu, C. Y., Liao, P. C., Proteomic profiling of human urinary proteome using nano-high performance liquid chromatography/electrospray ionization tandem mass spectrometry. Anal. Chim. Acta 2006, 579, 158-176.
132. Brand, J., Haslberger, T., Zolg, W., Pestlin, G., Palme, S., Depletion efficiency and recovery of trace markers from a multiparameter immunodepletion column. Proteomics 2006, 6, 3236-3242.
133. Zolotarjova, N., Martosella, J., Nicol, G., Bailey, J. et al., Differences among techniques for high-abundant protein depletion. Proteomics 2005, 5, 3304-3313.
134. Fang, X., Huang, L., Feitelson, J. S., Zhang, W., Affinity separation: divide and conquer the proteome. Drug Discov. Today Technol. 2004, 1, 141-148.
135. Pieper, R., Su, Q., Gatlin, C. L., Huang, S. T. et al., Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome. Proteomics 2003, 3, 422-432.
136. Bjorck, L., Kronvall, G., Purification and some properties of streptococcal protein G, a novel IgG-binding reagent. J. Immunol. 1984, 133, 969-974.
137. Lindmark, R., Thoren-Tolling, K., Sjoquist, J., Binding of immunoglobulins to protein A and immunoglobulin levels in mammalian sera. J. Immunol. Methods 1983, 62, 1-13.
138. Jmeian, Y., El Rassi, Z., Tandem affinity monolithic microcolumns with immobilized protein A, protein G', and antibodies for depletion of high abundance proteins from serum samples: integrated microcolumn-based fluidic system for simultaneous depletion and tryptic digestion. J. Proteome Res. 2007, 6, 947-954.
139. Maccarrone, G., Milfay, D., Birg, I., Rosenhagen, M. et al., Mining the human cerebrospinal fluid proteome by immunodepletion and shotgun mass spectrometry. Electrophoresis 2004, 25, 2402-2412.
140. Echan, L. A., Tang, H. Y., Ali-Khan, N., Lee, K., Speicher, D. W., Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics 2005, 5, 3292-3303.
141. Righetti, P. G., Boschetti, E., The ProteoMiner and the FortyNiners: searching for gold nuggets in the proteomic arena. Mass Spectrom. Rev. 2008, 27, 596-608.
142. Boschetti, E., Righetti, P. G., The ProteoMiner in the proteomic arena: a non-depleting tool for discovering low-abundance species. J. Proteomics 2008, 71, 255-264.
143. Sennels, L., Salek, M., Lomas, L., Boschetti, E. et al., Proteomic analysis of human blood serum using peptide library beads. J. Proteome Res. 2007, 6, 4055-4062.
144. Castagna, A., Cecconi, D., Sennels, L., Rappsilber, J. et al., Exploring the hidden human urinary proteome via ligand library beads. J. Proteome Res. 2005, 4, 1917-1930.
145. Antonioli, P., Fortis, F., Guerrier, L., Rinalducci, S. et al., Capturing and amplifying impurities from purified recombinant monoclonal antibodies via peptide library beads: a proteomic study. Proteomics 2007, 7, 1624-1633.
146. Righetti, P. G., Boschetti, E., Sherlock Holmes and the proteome - a detective story. FEBS J. 2007, 274, 897-905.
147. Hartwig, S., Czibere, A., Kotzka, J., Passlack, W. et al., Combinatorial hexapeptide ligand libraries (ProteoMiner): an innovative fractionation tool for differential quantitative clinical proteomics. Arch. Physiol. Biochem. 2009, 115, 155-160.
148. Righetti, P. G., Boschetti, E., Lomas, L., Citterio, A., Protein equalizer technology: the quest for a "democratic proteome". Proteomics 2006, 6, 3980-3992.
149. Bier, M., Recycling isoelectric focusing and isotachophoresis. Electrophoresis 1998, 19, 1057-1063.
150. Righetti, P. G., Castagna, A., Antonioli, P., Boschetti, E., Prefractionation techniques in proteome analysis: the mining tools of the third millennium. Electrophoresis 2005, 26, 297-319.
151. Gazzana, G., Borlak, J., Improved method for proteome mapping of the liver by 2-DE MALDI-TOF MS. J. Proteome Res. 2007, 6, 3143-3151.
152. Thorsell, A., Portelius, E., Blennow, K., Westman-Brinkmalm, A., Evaluation of sample fractionation using micro-scale liquid-phase isoelectric focusing on mass spectrometric identification and quantitation of proteins in a SILAC experiment. Rapid Commun. Mass Spectrom. 2007, 21, 771-778.
153. Lam, H. T., Antonioli, P., Righetti, P. G., Citterio, A., Girault, H., Gel-free IEF in a membrane-sealed multicompartment cell for proteome prefractionation. Electrophoresis 2007, 28, 1860-1866.
154. Bjellqvist, B., Ek, K., Righetti, P. G., Gianazza, E. et al., Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J. Biochem. Biophys. Methods 1982, 6, 317-339.
155. Tam, S., Electrophoretic prefractionation: new commercial tools from an old concept. Expert Rev. Proteomics 2006, 3, 379-381.
156. Sebastiano, R., Simo, C., Mendieta, M. E., Antonioli, P. et al., Mass distribution and focusing properties of carrier ampholytes for isoelectric focusing: I. Novel and unexpected results. Electrophoresis 2006, 27, 3919-3934.
157. Herbert, B., Righetti, P. G., A turning point in proteome analysis: sample prefractionation via multicompartment electrolyzers with isoelectric membranes. Electrophoresis 2000, 21, 3639-3648.
158. Zuo, X., Speicher, D. W., A method for global analysis of complex proteomes using sample prefractionation by solution isoelectrofocusing prior to two-dimensional electrophoresis. Anal. Biochem. 2000, 284, 266-278.
159. Richardson, M. R., Liu, S., Ringham, H. N., Chan, V., Witzmann, F. A., Sample complexity reduction for two-dimensional electrophoresis using solution isoelectric focusing prefractionation. Electrophoresis 2008, 29, 2637-2644.
160. Wang, H., Chang-Wong, T., Tang, H. Y., Speicher, D. W., Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomes. J. Proteome Res. 2010, 9, 1032-1040.
161. Fortis, F., Girot, P., Brieau, O., Castagna, A. et al., Isoelectric beads for proteome pre-fractionation. II: Experimental evaluation in a multicompartment electrolyzer. Proteomics 2005, 5, 629-638.
162. Myung, J. K., Lubec, G., Use of solution-IEF-fractionation leads to separation of 2673 mouse brain proteins including 255 hydrophobic structures. J. Proteome Res. 2006, 5, 1267-1275.
163. Zuo, X., Hembach, P., Echan, L., Speicher, D. W., Enhanced analysis of human breast cancer proteomes using micro-scale solution isoelectrofocusing combined with high resolution 1-D and 2-D gels. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2002, 782, 253-265.
164. Zhu, Y., Lubman, D. M., Narrow-band fractionation of proteins from whole cell lysates using isoelectric membrane focusing and nonporous reversed-phase separations. Electrophoresis 2004, 25, 949-958.
165. Heller, M., Michel, P. E., Morier, P., Crettaz, D. et al., Two-stage off-gel isoelectric focusing: protein followed by peptide fractionation and application to proteome analysis of human plasma. Electrophoresis 2005, 26, 1174-1188.
166. Michel, P. E., Crettaz, D., Morier, P., Heller, M. et al., Proteome analysis of human plasma and amniotic fluid by off-gel isoelectric focusing followed by nano-LC-MS/MS. Electrophoresis 2006, 27, 1169-1181.
167. Michel, P. E., Reymond, F., Arnaud, I. L., Josserand, J. et al., Protein fractionation in a multicompartment device using off-gel isoelectric focusing. Electrophoresis 2003, 24, 3-11.
168. Elschenbroich, S., Ignatchenko, V., Sharma, P., Schmitt-Ulms, G. et al., Peptide separations by on-line MudPIT compared to isoelectric focusing in an off-gel format: application to a membrane-enriched fraction from C2C12 mouse skeletal muscle cells. J. Proteome Res. 2009, 8, 4860-4869.
169. Waller, L. N., Shores, K., Knapp, D. R., Shotgun proteomic analysis of cerebrospinal fluid using off-gel electrophoresis as the first-dimension separation. J. Proteome Res. 2008, 7, 4577-4584.
170. Hubner, N. C., Ren, S., Mann, M., Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics 2008, 8, 4862-4872.
171. Horth, P., Miller, C. A., Preckel, T., Wenz, C., Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis. Mol. Cell Proteomics 2006, 5, 1968-1974.
172. Tan, A., Pashkova, A., Zang, L., Foret, F., Karger, B. L., A miniaturized multichamber solution isoelectric focusing device for separation of protein digests. Electrophoresis 2002, 23, 3599-3607.
173. Malmstrom, J., Lee, H., Nesvizhskii, A. I., Shteynberg, D. et al., Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. J. Proteome Res. 2006, 5, 2241-2249.
174. Zischka, H., Weber, G., Weber, P. J., Posch, A. et al., Improved proteome analysis of Saccharomyces cerevisiae mitochondria by free-flow electrophoresis. Proteomics 2003, 3, 906-916.
175. Islinger, M., Li, K. W., Loos, M., Liebler, S. et al., Peroxisomes from the heavy mitochondrial fraction: isolation by zonal free flow electrophoresis and quantitative mass spectrometrical characterization. J. Proteome Res. 2010, 9, 113-124.
176. Ellinger, I., Klapper, H., Courtoy, P. J., Vaerman, J. P., Fuchs, R., Different temperature sensitivity of endosomes involved in transport to lysosomes and transcytosis in rat hepatocytes: analysis by free-flow electrophoresis. Electrophoresis 2002, 23, 2117-2129.
177. Jethwaney, D., Islam, M. R., Leidal, K. G., de Bernabe, D. B. et al., Proteomic analysis of plasma membrane and secretory vesicles from human neutrophils. Proteome Sci. 2007, 5, 12.
178. Senis, Y. A., Tomlinson, M. G., Garcia, A., Dumon, S. et al., A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein. Mol. Cell Proteomics 2007, 6, 548-564.
179. Canut, H., Bauer, J., Weber, G., Separation of plant membranes by electromigration techniques. J. Chromatogr. B Biomed. Sci. Appl. 1999, 722, 121-139.
180. Barkla, B. J., Vera-Estrella, R., Hernandez-Coronado, M., Pantoja, O., Quantitative proteomics of the tonoplast reveals a role for glycolytic enzymes in salt tolerance. Plant Cell 2009, 21, 4044-4058.
181. Moritz, R. L., Clippingdale, A. B., Kapp, E. A., Eddes, J. S. et al., 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.
182. Weber, G., Wildgruber, R., Free-flow electrophoresis system for proteomics applications. Methods Mol. Biol. 2008, 384, 703-716.
183. Weber, G., Islinger, M., Weber, P., Eckerskorn, C., Volkl, A., Efficient separation and analysis of peroxisomal membrane proteins using free-flow isoelectric focusing. Electrophoresis 2004, 25, 1735-1747.
184. Hoffmann, P., Ji, H., Moritz, R. L., Connolly, L. M. et al., Continuous free-flow electrophoresis separation of cytosolic proteins from the human colon carcinoma cell line LIM 1215: a non two-dimensional gel electrophoresis-based proteome analysis strategy. Proteomics 2001, 1, 807-818.
185. Wang, Y., Hancock, W. S., Weber, G., Eckerskorn, C., Palmer-Toy, D., Free flow electrophoresis coupled with liquid chromatography-mass spectrometry for a proteomic study of the human cell line (K562/CR3). J. Chromatogr. A 2004, 1053, 269-278.
186. Xie, H., Onsongo, G., Popko, J., de Jong, E. P. et al., Proteomics analysis of cells in whole saliva from oral cancer patients via value-added three-dimensional peptide fractionation and tandem mass spectrometry. Mol. Cell Proteomics 2008, 7, 486-498.
187. Nissum, M., Kuhfuss, S., Hauptmann, M., Obermaier, C. et al., Two-dimensional separation of human plasma proteins using iterative free-flow electrophoresis. Proteomics 2007, 7, 4218-4227.
188. Foucher, A. L., Craft, D. R., Gelfand, C. A., Application of free flow electrophoresis to the analysis of the urine proteome. Methods Mol. Biol. 2010, 641, 27-45.
189. Kohlheyer, D., Eijkel, J. C., Schlautmann, S., van den Berg, A., Schasfoort, R. B., Microfluidic high-resolution free-flow isoelectric focusing. Anal. Chem. 2007, 79, 8190-8198.
190. Albrecht, J. W., El-Ali, J., Jensen, K. F., Cascaded free-flow isoelectric focusing for improved focusing speed and resolution. Anal. Chem. 2007, 79, 9364-9371.
191. Song, Y. A., Chan, M., Celio, C., Tannenbaum, S. R. et al., Free-flow zone electrophoresis of peptides and proteins in PDMS microchip for narrow pI range sample prefractionation coupled with mass spectrometry. Anal. Chem. 2010, 82, 2317-2325.
192. Wen, J., Wilker, E. W., Yaffe, M. B., Jensen, K. F., Microfluidic preparative free-flow isoelectric focusing: system optimization for protein complex separation. Anal. Chem. 2010, 82, 1253-1260.
193. Simpson, D. C., Smith, R. D., Combining capillary electrophoresis with mass spectrometry for applications in proteomics. Electrophoresis 2005, 26, 1291-1305.
194. Huang, Y. F., Huang, C. C., Hu, C. C., Chang, H. T., Capillary electrophoresis-based separation techniques for the analysis of proteins. Electrophoresis 2006, 27, 3503-3522.
195. Kolch, W., Neususs, C., Pelzing, M., Mischak, H., Capillary electrophoresis-mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery. Mass Spectrom. Rev. 2005, 24, 959-977.
196. Janini, G. M., Chan, K. C., Conrads, T. P., Issaq, H. J., Veenstra, T. D., Two-dimensional liquid chromatography-capillary zone electrophoresis-sheathless electrospray ionization-mass spectrometry: evaluation for peptide analysis and protein identification. Electrophoresis 2004, 25, 1973-1980.
197. Adkins, J. N., Varnum, S. M., Auberry, K. J., Moore, R. J. et al., Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell Proteomics 2002, 1, 947-955.
198. Jin, W. H., Dai, J., Li, S. J., Xia, Q. C. et al., Human plasma proteome analysis by multidimensional chromatography prefractionation and linear ion trap mass spectrometry identification. J. Proteome Res. 2005, 4, 613-619.
199. Aebersold, R., Morrison, H. D., Analysis of dilute peptide samples by capillary zone electrophoresis. J. Chromatogr. 1990, 516, 79-88.
200. Monton, M. R., Terabe, S., Field-enhanced sample injection for high-sensitivity analysis of peptides and proteins in capillary electrophoresis-mass spectrometry. J. Chromatogr. A 2004, 1032, 203-211.
201. Imami, K., Monton, M. R., Ishihama, Y., Terabe, S., Simple on-line sample preconcentration technique for peptides based on dynamic pH junction in capillary electrophoresis-mass spectrometry. J. Chromatogr. A 2007, 1148, 250-255.
202. Monton, M. R., Terabe, S., Sample enrichment techniques in capillary electrophoresis: focus on peptides and proteins. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2006, 841, 88-95.
203. Madajova, V., Simunicova, E., Kaniansky, D., Marak, J., Zelenska, V., Fractionation of glycoforms of recombinant human erythropoietin by preparative capillary isotachophoresis. Electrophoresis 2005, 26, 2664-2673.
204. Zhang, H., Hunter, G. K., Goldberg, H. A., Lajoie, G. A., Yeung, K. K., An integrated procedure of selective injection, sample stacking and fractionation of phosphopeptides for MALDI MS analysis. Anal. Chim. Acta 2007, 581, 268-280.
205. Schmitt-Kopplin, P., Frommberger, M., Capillary electrophoresis-mass spectrometry: 15 years of developments and applications. Electrophoresis 2003, 24, 3837-3867.
206. Shen, Y., Berger, S. J., Anderson, G. A., Smith, R. D., High-efficiency capillary isoelectric focusing of peptides. Anal. Chem. 2000, 72, 2154-2159.
207. Chen, J., Lee, C. S., Shen, Y., Smith, R. D., Baehrecke, E. H., Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separation. Electrophoresis 2002, 23, 3143-3148.
208. Zhou, F., Hanson, T. E., Johnston, M. V., Intact protein profiling of Chlorobium tepidum by capillary isoelectric focusing, reversed-phase liquid chromatography, and mass spectrometry. Anal. Chem. 2007, 79, 7145-7153.
209. Dai, L., Li, C., Shedden, K. A., Misek, D. E., Lubman, D. M., Comparative proteomic study of two closely related ovarian endometrioid adenocarcinoma cell lines using cIEF fractionation and pathway analysis. Electrophoresis 2009, 30, 1119-1131.
210. Wang, W., Guo, T., Rudnick, P. A., Song, T. et al., Membrane proteome analysis of microdissected ovarian tumor tissues using capillary isoelectric focusing/reversed-phase liquid chromatography-tandem MS. Anal. Chem. 2007, 79, 1002-1009.
211. Wasinger, V., Ly, L., Fitzgerald, A., Walsh, B., Prefractionation, enrichment, desalting and depleting of low volume and low abundance proteins and peptides using the MF10. Methods Mol. Biol. 2008, 424, 257-275.
212. Ly, L., Wasinger, V. C., Peptide enrichment and protein fractionation using selective electrophoresis. Proteomics 2008, 8, 4197-4208.
213. Ly, L., Wasinger, V. C., Mass and charge selective protein fractionation for the differential analysis of T-cell and CD34+ stem cell proteins from cord blood. J. Proteomics 2010, 73, 571-578.