Recent advances in proteolysis and peptide/protein separation by chromatographic strategies

Science China Chemistry

Volumn 53, Issue 4, 2010, Pages 685-694

  Zhang, Xiang Min ^a   Liu, Bao Hong ^a   Zhang, Li Hua ^a   Zou, Han Fa ^a   Cao, Jing ^a   Gao, Ming Xia ^a   Tang, Jia ^a   Liu, Yun ^a   Yang, Peng Yuan ^a   Zhang, Yu Kui ^a  

^a FUDAN UNIVERSITY   (China)

Author keywords

Chromatographic separation; Enzymatic digestion; Mass spectrometry; Peptide enrichment; Proteolysis

Indexed keywords

BOTTOM UP APPROACH; CHROMATOGRAPHIC SEPARATIONS; ENZYMATIC DIGESTION; ENZYMATIC DIGESTIONS; MICRO-REACTOR; PEPTIDE SEPARATION; PROTEOLYTIC REACTION; PROTEOMICS; SEPARATION AND IDENTIFICATION; TOP-DOWN APPROACH;

BATCH REACTORS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; REACTION RATES; RESEARCH;

PEPTIDES;

EID: 77953296633     PISSN: 16747291     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11426-010-0135-7     Document Type: Review

References (65)

1. Svec F. Less common applications of monoliths: I. Microscale protein mapping with proteolytic enzymes immobilized on monolithic supports. Electrophoresis, 2006, 27: 947-961;
2. Krênková J, Foret F. Immobilized microfluidic enzymatic reactors. Electrophoresis, 2004, 25: 3550-3563 (Pubitemid 40012112)
3. Wang H, Hanash S. Multi-dimensional liquid phase based separations in proteomics. J Chromatogr B, 2003, 787: 11-18 (Pubitemid 36351262)
4. Licklider L, Kuhr WG. Characterization of reaction dynamics in a trypsin-modified capillary microreactor. Anal Chem, 1998, 70: 1902-1908 (Pubitemid 128484594)
5. Guo Z, Zhang QC, Lei ZD, Kong L, Mao XQ, Zou HF. Studies on rapid micro-scale peptide mapping analysis using a capillary micro- reactor. Chem J Chin Univ, 2002, 23: 1277-1280 (Pubitemid 135709242)
6. Guo Z, Xu SY, Lei ZD, Zou HF, Guo BC. Immobilized metal-ion chelating capillary microreactor for peptide mapping analysis of proteins by matrix assisted laser desorption/ionization-time of flightmass spectrometry. Electrophoresis, 2003, 24: 3633-3639 (Pubitemid 38089165)
7. Bossi A, Guizzardi L, D'Acuto MR, Righetti PG. Controlled enzyme-immobilisation on capillaries for microreactors for peptide mapping. Anal Bioanal Chem, 2004, 378: 1722-1728 (Pubitemid 40877649)
8. Kim J, Grate JW, Wang P. Nanostructures for enzyme stabilization. Chem Eng Sci, 2006, 61: 1017-1026 (Pubitemid 41655855)
9. Fan J, Shui WQ, Yang PY, Wang XY, Xu YM, Wang HH, Chen X, Zhao DY. Mesoporous silica nanoreactors for highly efficient proteolysis. Chem Eur J, 2005, 11: 5391-5396 (Pubitemid 41285094)
10. Li Y, Xu XQ, Yan B, Deng CH, Yu WJ, Yang PY, Zhang XM. microchip reactor packed with metal-ion chelated magnetic silica microspheres for highly efficient proteolysis. J Proteome Res, 2007, 6: 2367-2375 (Pubitemid 46985124)
11. Liu Y, Xue Y, Ji J, Chen X, Kong JL, Yang PY, Girault HH, Liu BH. Gold nanoparticle assembly microfluidic reactor for efficient on-line proteolysis. Mol Cel Proteomics, 2007, 6: 1428-1436 (Pubitemid 47365440)
12. Qian K, Wan JJ, Qiao L, Huang XD, Tang JW, Wang YH, Kong JL, Yang PY, Yu CZ, Liu BH, Macroporous materials as novel catalysts for efficient and controllable proteolysis. Anal Chem, 2009, 81(14): 5749-5756
13. Bi HY, Qiao L, Busnel J-M, Liu BH, Girault HH. Kinetics of proteolytic reactions in nanoporous materials. J Proteome Res, 2009, 8: 4685-4692
14. Josic D, Clifton JG. Use of monolithic supports in proteomics technology. J Chromatogr A, 2007, 1144: 2-13 (Pubitemid 46298853)
15. Zhu GJ, Zhang LH, Yuan HM, Liang Z, Zhang WB, Zhang YK. Recent development of monolithic materials as matrices in microcolumn separation systems. J Sep Sci, 2007, 3: 792-803 (Pubitemid 46736400)
16. Krenková J, Bilková Z, Foret F. Chararacterization of a monolithic immobilized trypsin microreactor with on-line coupling to ESI-MS. J Sep Sci, 2005, 28: 1675-1684 (Pubitemid 43055011)
17. Duan JC, Sun LL, Liang Z, Zhang J, Wang H, Zhang LH, Zhang WB, Zhang YK. Rapid protein digestion and identification using monolithic enzymatic microreactor coupled with nano-liquid chromatography- electrospray ionization mass spectrometry. J Chromatogr A, 2006, 1106: 165-174 (Pubitemid 43145848)
18. Duan JC, Liang Z, Yang C, Zhang J, Zhang LH, Zhang WB, Zhang YK. Rapid protein identification using monolithic enzymatic microreactor and LC-ESI-MS/MS. Proteomics, 2006, 6: 412-419 (Pubitemid 43208020)
19. Ye ML, Hu S, Schoenherr RM, Dovichi NJ. On-line protein digestion and peptide mapping by capillary electrophoresis with post-column labeling for laser-induced fluorescence detection. Electrophoresis, 2004, 25: 1319-1326 (Pubitemid 38801650)
20. Feng S, Ye ML, Jiang XG, Jin WH, Zou HF. Coupling the immobilized trypsin microreactor of monolithic capillary with μRPLCMS/ MS for shotgun proteome analysis. J Proteome Res, 2006, 5: 422-428 (Pubitemid 43222311)
21. Jiang HH, Zou HF, Wang HL, Ni JY, Zhang Q, Zhang YK. On-line characterization of the activity and reaction kinetics of immobilized enzyme by high-performance frontal analysis. J Chromatogr A, 2000, 903: 77-84
22. Tyan YC, Jong SB, Liao JD, Liao PC, Yang MH, Liu CY, Klauser R, Himmelhaus M, Grunze M. proteomic profiling of erythrocyte proteins by proteolytic digestion chip and identification using twodimensional electrospray ionization tandem mass spectrometry. J Proteome Res, 2005, 4: 748-757 (Pubitemid 40863264)
23. Liu Y, Lu HJ, Zhong W, Song PY, Kong JL, Yang PY, Girault HH, Liu BH. Multilayer-assembled microchip for enzyme immobilization as reactor toward low-level protein identification. Anal Chem, 2006, 78: 801-808 (Pubitemid 43228588)
24. Jin W, Brennan JD. Properties and applications of proteins encapsulated within sol-gel derived materials. Anal Chim Acta, 2002, 461: 1-36 (Pubitemid 34603555)
25. Liu Y, Xue Y, Ji J, Chen X, Kong JL, Yang PY, Girault HH, Liu BH. Gold nanoparticle assembly microfluidic reactor for efficient on-line proteolysis. Mol Cell Proteomics, 2007, 6: 1428-1436 (Pubitemid 47365440)
26. Liu Y, Qu HY, Xue Y, Yang PY, Liu BH. Enhancement of proteolysis through the silica-gel-derived microfluidic reactor. Proteomics, 2007, 7: 1373-1378 (Pubitemid 46775872)
27. Ekstrom S, Onnerfjord P, Nilsson J, Bengtsson M, Laurell T, Marko-Varga G. integrated microanalytical technology enabling rapid and automated protein identification. Anal Chem, 2000, 72: 286-293 (Pubitemid 30051884)
28. Liu Y, Zhong W, Meng S, Kong JL, Lu HJ, Yang PY, Girault HH, Liu BH. Assembly-controlled biocompatible interface on a microchip: strategy to highly efficient proteolysis. Chem Eur J, 2006, 12: 6585-6591 (Pubitemid 44366706)
29. Wu HL, Zhai JJ, Tian YP, Lu HJ, Wang XY, Jia WT, Liu BH, Yang PY, Xu YM, Wang HH. Microfluidic enzymatic-reactors for peptide mapping: strategy, characterization, and performance. Lab Chip, 2004, 4: 588-597
30. Xu ZR, Fang ZL. Composite poly(dimethylsiloxane)/glass microfluidic system with an immobilized enzymatic particle-bed reactor and sequential sample injection for chemiluminescence determinations. Anal Chim Acta, 2004, 507: 129-135
31. Yu T, Zhang YH, You CP, Zhuang JH, Wang B, Liu BH, Kang YJ, Tang Y. Controlled nanozeolite-assembled electrode: remarkable enzyme- immobilization ability and high sensitivity as biosensor. Chem Eur J, 2006, 12: 1137-1143 (Pubitemid 43145161)
32. Washburn MP, Walters D, Yates III JR. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol, 2001, 19: 242-247 (Pubitemid 32220565)
33. Dai J, Shieh CH, Sheng Q, Zhou H, Zeng R. Proteomic analysis with integrated multiple dimensional liquid chromatography/mass spectrometry based on elution of ion exchange column using pH steps. Anal Chem, 2005, 77: 5793-5799 (Pubitemid 41324277)
34. Dai J, Jin W, Sheng Q, Shieh C, Wu J, Zeng R. Protein phosphorylation and expression profiling by yin-yang multidimensional liquid chromatography (yin-yang mdlc) mass spectrometry. J Proteome Res, 2007, 6: 250-262 (Pubitemid 46173677)
35. Jiang X, Feng S, Tian R, Han G, Jiang X, Ye M, Zou H. Automation of nanoflow liquid chromatography-tandem mass spectrometry for proteome analysis by using a strong cation exchange trap column. Proteomics, 2007, 7: 528-539 (Pubitemid 46362616)
36. Wang F, Jiang X, Feng S, Tian R, Jiang X, Han G, Liu H, Ye M, Zou H. Automated injection of uncleaned samples using a ten-port switching valve and a strong cation-exchange trap column for proteome analysis. J Chromatogr A, 2007, 1171: 56-62 (Pubitemid 47588274)
37. Nice EC, Rothacker J, Weinstock J, Lim L, Catimel B. Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomics analysis. J Chromatogr A, 2007, 1168: 190-210 (Pubitemid 47488327)
38. Bedani F, Kok W, Janssen H. A theoretical basis for parameter selection and instrument design in comprehensive size-exclusion chromatography × liquid chromatography. J Chromatogr A, 2006, 1133: 126-134 (Pubitemid 44604375)
39. Wang J, Jiang Y, Jiang H, Cai Y, Qian X. Phosphopeptide detection using automated online IMAC-capillary LC-ESI-MS/MS. Proteomics, 2006, 6: 404-411 (Pubitemid 43208019)
40. Madera M, Mechref Y, Klouckova I, Novotny MV. 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 (Pubitemid 44330828)
41. Ma JF, Liu JX, Sun LL, Gao L, Liang Z, Zhang LH, Zhang YK. Online integration of multiple sample pretreatment steps involving denaturation, reduction, and digestion with microflow reversed-phase liquid chromatography-electrospray ionization tandem mass spectrometry for high-throughput proteome profiling. Anal Chem, 2009, 81: 6534-6540
42. Yuan HM, Zhou Y, Zhang LH, Liang Z, Zhang YK. Integrated protein analysis platform based on column switch recycling size exclusion chromatography, microenzymatic reactor and μRPLC-ESIMS/ MS. J Chromatogr A, 2009, 1216: 7478-7482
43. Zhang J, Xu X, Shen H, Zhang X. Analysis of nuclear proteome in C57 mouse liver tissue by a nano-flow 2-D-LC-ESI-MS/MS approach. J Sep Sci, 2006, 29: 2635-2646 (Pubitemid 46040159)
44. Zhang J, Xu X, Gao M, Yang P, Zhang X. Comparison of 2-D LC and 3-D LC with post- and pre-tryptic-digestion SEC fractionation for proteome analysis of normal human liver tissue. Proteomics, 2007, 7: 500-512 (Pubitemid 46362613)
45. Cao R, Zhang L, Nie S, Wang X, Liang S. Analysis of mouse liver plasma membrane proteins by multidimensional liquid chromatography-tandem mass spectrometry. Chin J Biochem Mol Bio, 2005, 21: 134-142 (Pubitemid 41739929)
46. Zhang Y, Shi R, Meng Q, Wang J. Studies on a novel and large-scale proteomics method and its application. Chin J Anal Chem, 2005, 33: 1371-1375 (Pubitemid 41597661)
47. Jiang X, Zhou H, Zhang L, Sheng Q. A high-throughput approach for subcellular proteome- Identification of rat liver proteins using subcellular fractionation coupled with two-dimensional liquid chromatography tandem mass spectrometry and bioinformatic analysis. Mole Cell Proteomics, 2004, 3.5: 441-455 (Pubitemid 38714286)
48. Zeng R, Ruan H, Jiang X, Zhou H. Proteomic analysis of SARS associated coronavirus using two-dimensional liquid chromatography mass spectrometry and one-dimensional sodium dodecyl sulfatepolyacrylamide gel electrophoresis followed by mass spectroemtric analysis. J Proteome Res, 2004, 3: 549-555 (Pubitemid 39207359)
49. Chinese Human Liver Proteome Profiling Consortium. J Proteome Res, 2010, 9: 79-94
50. Horn A, Kreusch S, Bublitz R, Hoppe H, Cumme GA, Schulze M, Moore T, Ditze G, Rhode H. Multidimensional proteomics of human serum using parallel chromatography of native constituents and microplate technology. Proteomics, 2006, 6: 559-570 (Pubitemid 43208035)
51. Liu C, Zhang X. Multidimensional capillary array liquid chromatography and matrix-assisted laser desorption/ionization tandem mass spectrometry for high-throughput proteomic analysis. J Chromatogr A, 2007, 1139: 191-198 (Pubitemid 44937270)
52. Gu X, Deng C, Yan G, Zhang X. Capillary array reversed-phase liquid chromatography-based multidimensional separation system coupled with MALDI-TOF-TOF-MS detection for high-throughput proteome analysis. J Proteome Res, 2006, 5: 3186-3196 (Pubitemid 44749236)
53. Jin W, Dai J, Li S, Xia Q, Zou HF, Zeng R. Human plasma proteome analysis by multidimensional chromatography prefractionation and linear ion trap mass spectrometry identification. J Proteome Res, 2005, 4: 613-619 (Pubitemid 40548171)
54. Sharma S, Simpson DC, Tolic N, Jaitly N, Mayampurath AM, Smith RD, Pasa-Tolic L. Proteomic profiling of intact proteins using wax-rplc 2-D separations and fticr mass spectrometry. J Proteome Res, 2007, 6: 602-610 (Pubitemid 46340164)
55. Rothemund DL, Locke VL, Liew A, Thomas TM, Wasinger V, Rylatt DB. Depletion of the highly abundant protein albumin from human plasma using the Gradiflow. Proteomics, 2003, 3: 279-287 (Pubitemid 36343684)
56. Wasinger VC, Locke VL, Raftery MJ, Larance M, Rothemund D, Liew A, Bate I, Guilhaus M. Two-dimensional liquid chromatography/ tandem mass spectrometry analysis of GradiflowTM fractionated native human plasma. Proteomics, 2005, 5: 3397-3401 (Pubitemid 41192045)
57. Gao M, Zhang J, Deng C, Yang P, Zhang X. Novel strategy of high-abundance protein depletion using multidimensional liquid chromatography. J Proteome Res, 2006, 5: 2853-2860 (Pubitemid 44604233)
58. Li X, Gong Y, Wu S, Cai Y, He P, Lu Z, Ying W, Zhang Y, Jiao L, He H, Zhang Z, He F, Zhao X, Qian X. Comparison of alternative analytical techniques for the characterisation of the human serum proteome in HUPO Plasma Proteome Project. Proteomics, 2005, 5: 3423-3441 (Pubitemid 41192048)
59. Lohaus C, Nolte A, Blüggel M, Scheer C, Klose J, Gobom J, Schüler A, Wiebringhaus T, Meyer HE, Marcus K. Multidimensional chromatography: a powerful tool for the analysis of membrane proteins in mouse brain. J Proteome Res, 2007, 6: 105-113 (Pubitemid 46178016)
60. Qin L, He XW, Zhang W, Li WY, Zhang YK. Macroporous thermosensitive imprinted hydrogel for recognition of protein by metal coordinate interaction. Anal Chem, 2009, 81: 7206-7216
61. Zhu GJ, Yuan HM, Zhao P, Zhang LH, Liang Z, Zhang WB, Zhang YK. Macroporous polyacrylamide-based monolithic column with immobilized pH gradient for protein analysis. Electrophoresis, 2006, 27: 3578-3583 (Pubitemid 44515595)
62. Han B, Wang PL, Zhu GJ, Zhang LH, Qu F, Deng YL, Zhang YK. Microchip free flow isoelectric focusing for protein prefractionation using monolith with immobilized pH gradient. J Sep Sci, 2009, 32: 1211-1215
63. Yuan HM, Zhang LH, Zhang WB, Liang Z, Zhang YK. Columns switch recycling size exclusion chromatography for high resolution protein separation. J Chromatogr A, 2009, 1216: 7024-7032
64. Gu X, Wang Y, Zhang XM. Large-bore particle-entrapped monolithic precolumns prepared by a sol-gel method for on-line peptides trapping and preconcentration in multidimensional liquid chromatography system for proteome analysis. J ChromatogrA, 2005, 1072: 223-232 (Pubitemid 40501913)
65. Zhang XM, Huang S. Single step on-column frit making for capillary high-performance liquid chromatography using sol-gel technology. J Chromatogr A, 2001, 910: 13-18 (Pubitemid 32112705)