Multicolumn separation platform for simultaneous depletion and prefractionation prior to 2-DE for facilitating in-depth serum proteomics profiling

Journal of Proteome Research

Volumn 8, Issue 10, 2009, Pages 4592-4603

  Jmeian, Yazen ^a   El Rassi, Ziad ^a  

^a OKLAHOMA STATE UNIVERSITY   (United States)

Author keywords

2 DE; Affinity LC; Immobilized metal ion affinity chromatography; Multidimensional LC; Proteomics

Indexed keywords

ANAZOLENE SODIUM; COPPER; DIGLYCINE; FLUORESCENT DYE; NICKEL; PROTEIN A; PROTEIN G; ZINC;

ARTICLE; HUMAN; IMMOBILIZED METAL AFFINITY CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEPLETION; PROTEIN IMMOBILIZATION; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; SEPARATION TECHNIQUE; TWO DIMENSIONAL GEL ELECTROPHORESIS;

BLOOD PROTEINS; CHROMATOGRAPHY, AFFINITY; CHROMATOGRAPHY, LIQUID; COPPER; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; IMINO ACIDS; MASS SPECTROMETRY; NICKEL; PROTEOME; PROTEOMICS; ZINC;

EID: 70349973294     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900399q     Document Type: Article

References (41)

1. Faca, V.; Pitteri Sharon, J.; Newcomb, L.; Glukhova, V.; Phanstiel, D.; Krasnoselsky, A.; Zhang, Q.; Struthers, J.; Wang, H.; Eng, J.; Fitzgibbon, M.; McIntosh, M.; Hanash, S. Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J. Proteome Res. 2007, 6, 3558-3565. (Pubitemid 47522747)
2. Plavina, T.; Wakshull, E.; Hancock, W. S.; Hincapie, M. Combination of abundant protein depletion and multi-lectin affinity chromatography (M-LAC) for plasma protein biomarker discovery. J. Proteome Res. 2007, 6, 662-671. (Pubitemid 46340170)
3. Jmeian, Y.; El Rassi, Z. Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids for in-depth proteomics analysis. Electrophoresis 2009, 30, 249-261.
4. Righetti, P. G.; Castagna, A.; Herbert, B.; Reymond, F.; Rossier, J. S. Prefractionation techniques in proteome analysis. Proteomics 2003, 3, 1397-1407.
5. Pieper, R.; Su, Q.; Gatlin, C. L.; Huang, S.-T.; Anderson, N. L.; Steiner, S. Multi-component immunoaffinity subtraction chromatography: An innovative step towards a comprehensive survey of the human plasma proteome. Proteomics 2003, 3, 422-432. (Pubitemid 36428295)
6. 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.
7. Righetti, P. G.; Boschetti, E.; Lomas, L.; Citterio, A. Protein Equalizer Technology: the quest for a "democratic proteome". Proteomics 2006, 6, 3980-3992.
8. Jmeian, Y.; El Rassi, Z. Micro-high-performance liquid chromatography platform for the depletion of high-abundance proteins and subsequent on-line concentration/capturing of medium and low-abundance proteins from serum. Application to profiling of protein expression in healthy and osteoarthritis sera by 2-D gel electrophoresis. Electrophoresis 2008, 29, 2801-2811. (Pubitemid 352006114)
9. 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. (Pubitemid 40253785)
10. Tang, J.; Gao, M.; Deng, C.; Zhang, X. Recent development of multidimensional chromatography strategies in proteome research. J. Chromatogr., B 2008, 866, 123-132.
11. Hoffman, S. A.; Joo, W. A.; Echan, L. A.; Speicher, D. W. Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma. J. Chromatogr., B 2007, 849, 43-52.
12. 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.
13. Zolotarjova, N.; Mrozinski, P.; Chen, H.; Martosella, J. Combination of affinity depletion of abundant proteins and reversed-phase fractionation in proteomic analysis of human plasma/serum. J. Chromatogr., A 2008, 1189, 332-338.
14. Martosella, J.; Zolotarjova, N. Multi-component immunoaffinity subtraction and reversed-phase chromatography of human serum. Methods Mol. Biol. 2008, 425, 27-39.
15. Madera, M.; Mechref, Y.; Klouckova, I.; Novotny, M. V. High-sensitivity profiling of glycoproteins from human blood serum through multiple-lectin affinity chromatography and liquid chromatography/tandem mass spectrometry. J. Chromatogr., B 2007, 845, 121-137.
16. Madera, M.; Mechref, Y.; Klouckova, I.; Novotny, M. V. Semiautomated high-sensitivity profiling of human blood serum glycoproteins through lectin preconcentration and multidimensional chromatography/tandem mass spectrometry. J. Proteome Res. 2006, 5, 2348-2363.
17. Stalder, D.; Haeberli, A.; Heller, M. Evaluation of reproducibility of protein identification results after multidimensional human serum protein separation. Proteomics 2008, 8, 414-424. (Pubitemid 351252001)
18. Moritz, R. L.; Clippingdale, A. B.; Kapp, E. A.; Eddes, J. S.; Ji, H.; Gilbert, S.; Connolly, L. M.; 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.
19. Tang, H. Y.; Ali-Khan, N.; Echan, L. A.; Levenkova, N.; Rux, J. J.; Speicher, D. W. 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.
20. Bedair, M.; El Rassi, Z. Affinity chromatography with monolithic capillary columns. 1. Polymethacrylate monoliths with immobilized mannan for the separations of mannose binding proteins by capillary electrochromatography and nano-scale liquid chromatography. J. Chromatogr., A 2004, 1004, 177-186. (Pubitemid 38953988)
21. Bedair, M.; El Rassi, Z. Affinity chromatography with monolithic capillary columns. II Polymethacrylate monoliths with immobilized lectins for the separation of glycoconjugates by nano-liquid affinity chromatography. J. Chromatogr., A 2005, 1079, 236-245. (Pubitemid 40813205)
22. 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. (Pubitemid 46480459)
23. Okanda, F.; El Rassi, Z. Affinity monolithic capillary columns for glycomics/proteomics 1. Polymethacrylate monoliths with immobilized lectins for glycoprotein separation by affinity capillary electrochromatography and affinity nano-liquid chromatography in either a single column or columns coupled in series. Electrophoresis 2006, 27, 1020-1030.
24. Porath, J.; Carlsson, J.; Olsson, I.; Belfrage, G. Metal chelate affinity chromatography, a new approach to protein fractionation. Nature 1975, 258, 598-599.
25. Gooding, K. M.; El Rassi, Z.; Horvath, C. Metal interaction chromatography. In HPLC of Biological Macromolecules, 2nd ed.; Gooding, K. M., Regnier, F. E. , Eds.; Marcel Dekker: New York, 2002; Vol.87, pp 247-280.
26. Porath, J.; Olin, B. Immobilized metal ion affinity adsorption and immobilized metal ion affinity chromatography of biomaterials. Serum protein affinities for gel-immobilized iron and nickel ions. Biochemistry 1983, 22, 1621-1630.
27. Porath, J. IMAC--Immobilized metal ion affinity based chromatography. Trends Anal. Chem. 1988, 7, 254-259. (Pubitemid 18660387)
28. Sulkowski, E. The saga of IMAC and MIT. BioEssays 1989, 10, 170-175.
29. Sulkowski, E. Purification of proteins by IMAC. Trends Biotechnol. 1985, 3, 1-7.
30. Hemdan, E. S.; Zhao, Y. J.; Sulkowski, E.; Porath, J. Surface topography of histidine residues: a facile probe by immobilized metal ion affinity chromatography. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 1811-1815. (Pubitemid 19087023)
31. Scopes, R. K. Separation by adsorption II: ion exchangers and nonspecific adsorption. In Protein Purification: Principles and Practice, 3rd ed.; Springer-Verlag: New York, 1994; pp 180-183.
32. Corradini, D.; el Rassi, Z.; Horvath, C.; Guerra, G.; Horne, W. Combined lectin-affinity and metal-interaction chromatography for the separation of glycophorins by high-performance liquid chromatography. J. Chromatogr. 1988, 458, 1-11.
33. Luo, Q.; Zou, H.; Xiao, X.; Guo, Z.; Kong, L.; Mao, X. Chromatographic separation of proteins on metal immobilized iminodiacetic acid-bound molded monolithic rods of macroporous poly(glycidyl methacrylate-co-ethylene dimethacrylate). J. Chromatogr., A 2001, 926, 255-264. (Pubitemid 32744730)
34. Chromy, B. A.; Gonzales, A. D.; Perkins, J.; Choi, M. W.; Corzett, M. H.; Chang, B. C.; Corzett, C. H.; McCutchen-Maloney, S. L. Proteomic analysis of human serum by two-dimensional differential gel electrophoresis after depletion of high-abundant proteins. J. Proteome Res. 2004, 3, 1120-1127. (Pubitemid 40040365)
35. Zolotarjova, N.; Martosella, J.; Nicol, G.; Bailey, J.; Boyes, B. E.; Barrett, W. C. Differences among techniques for high-abundant protein depletion. Proteomics 2005, 5, 3304-3313.
36. Al-Mashikhi, S. A.; Nakai, S. Separation of immunoglobulin and transferrin from blood serum and plasma by metal chelate interaction chromatography. J. Dairy Sci. 1988, 71, 1756-1763.
37. Andersen, T.; Munthe-Fog, L.; Garred, P.; Jacobsen, S. Serum levels of ficolin-3 (Hakata antigen) in patients with systemic lupus erythematosus. J. Rheumatol. 2009, 36, 757-759.
38. Wong, J. C.; Holland, J.; Parsons, T.; Smith, A.; Williams, P. Identification and characterization of an iron-regulated hemopexin receptor in Haemophilus influenzae type b. Infect. Immun. 1994, 62, 48-59. (Pubitemid 24011939)
39. Mauk, M. R.; Rosell, F. I.; Lelj-Garolla, B.; Moore, G. R.; Mauk, A. G. Metal ion binding to human hemopexin. Biochemistry 2005, 44, 1864-1871.
40. Janssen, B. J.; Huizinga, E. G.; Raaijmakers, H. C.; Roos, A.; Daha, M. R.; Nilsson-Ekdahl, K.; Nilsson, B.; Gros, P. Structures of complement component C3 provide insights into the function and evolution of immunity. Nature 2005, 437, 505-511. (Pubitemid 41613542)
41. She, Y. M.; Narindrasorasak, S.; Yang, S.; Spitale, N.; Roberts, E. A.; Sarkar, B. Identification of metal-binding proteins in human hepatoma lines by immobilized metal affinity chromatography and mass spectrometry. Mol. Cell. Proteomics 2003, 2, 1306-1318.