Citation: WEI Liming, LU Haojie, YANG Pengyuan, WU Xin. Development of sample pretreatment approach and technology for peptidome[J]. Chinese Journal of Chromatography, ;2013, 31(7): 603-612. doi: 10.3724/SP.J.1123.2013.05030 shu

Development of sample pretreatment approach and technology for peptidome

WEI Liming ¹ ,
LU Haojie ¹ ,
YANG Pengyuan ¹ ,
WU Xin ^2,,

1.
1. Institutes of Biomedical Sciences & Department of Chemistry, Fudan University, Shanghai 200032, China;

Corresponding author: WU Xin,
Received Date: 20 May 2013

Fund Project: 国家杰出青年科学基金项目(21025519). (21025519)

As a branch of proteomics, peptidome has been extensively applied in biomarker discovery, early diagnosis and pharmacy. In the research of peptidome, sample pretreatment plays a vital role. Here, we review the pretreatment approaches and techniques of peptidome, mainly including ultrafiltration, organic solvent precipitation, solid phase extraction and so on. The biggest challenge of the development of peptidome is the large number of high-abundance proteins in the sample. Therefore, there is an urgent need to develop the fast, efficient, high-throughput and automated sample preparation methods and techniques.
- peptidome,
- low-molecular weight proteins,
- peptides,
- sample pretreatment
1. [1]
  [1] Robinson W H, Steinman L. Nat Biotech, 2011, 29(6): 500
2. [2]
  [2] Hölttä M, Zetterberg H, Mirgorodskaya E, et al. PLoS ONE, 2012, 7(8): e42555
3. [3]
  [3] Larman H B, Zhao Z, Laserson U, et al. Nat Biotech, 2011, 29(6): 535
4. [4]
  [4] Gelman J S, Sironi J, Castro L M, et al. J Proteome Res, 2011, 10(4): 1583
5. [5]
  [5] Soloviev M, Finch P. Proteomics, 2006, 6(3): 744
6. [6]
  [6] Villanueva J, Shaffer D R, Philip J, et al. J Clin Inverst, 2006, 116(1): 271http://www.ncbi.nlm.nih.gov/pubmed/16395409#
7. [7]
  [7] Chertov O, Simpson J T, Biragyn A, et al. Expert Rev Proteomics, 2005, 2(1): 139
8. [8]
  [8] Hu L, Ye M, Zou H. Expert Rev Proteomics, 2009, 6(4): 433
9. [9]
  [9] West-Norager M, Kelstrup C D, Schou C, et al. J Chromatogr B, 2007, 847(1): 30
10. [10]
  [10] Hsieh S Y, Chen R Y, Pan Y H, et al. Proteomics, 2006, 6(10): 3189
11. [11]
  [11] Di Girolamo F, Alessandroni J, Somma P, et al. J Proteomics, 2010, 73(3): 667
12. [12]
  [12] Banks R E, Stanley A J, Cairns D A, et al. Clin Chem, 2005, 51(9): 1637
13. [13]
  [13] Zimmerman L J, Li M, Yarbrough W G, et al. Mol Cell Proteomics, 2012, 11(6): 1http://www.keepthefaith1296.com/parkinsons/interlaboratory-study-characterizing-a-yeast-performance-standard-for-benchmarking-lc-ms-platform-performance-MTk4NTg0OTk=.htm
14. [14]
  [14] de Jong E P, van Riper S K, Koopmeiners J S, et al. Clin Chim Acta, 2011, 412(23/24): 2284http://www.keepthefaith1296.com/parkinsons/development-and-evaluation-of-normalization-methods-for-label-free-relative-quantification-of-endogenous-peptides-MTk1OTY2OTU=.htm
15. [15]
  [15] Scholz B, Sköld K, Kultima K, et al. Mol Cell Proteomics, 2011, 10(3): 1http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517140/
16. [16]
  [16] Zhou M, Lucas D A, Chan K C, et al. Electrophoresis, 2004, 25(9): 1289
17. [17]
  [17] Tirumalai R S, Chan K C, Prieto D A, et al. Mol Cell Proteomics, 2003, 2(10): 1096
18. [18]
  [18] Kawashima Y, Fukutomi T, Tomonaga T, et al. J Proteome Res, 2010, 9(4): 1694
19. [19]
  [19] Vitorino R, Guedes S, Manadas B, et al. J Proteomics, 2012, 75(17): 5140
20. [20]
  [20] Good D M, Zürbig P, Argilés A, et al. Mol Cell Proteomics, 2010, 9(11): 2424
21. [21]
  [21] Ziganshin R, Arapidi G, Azarkin I, et al. J Proteomics, 2011, 74(5): 595
22. [22]
  [22] Fan N J, Gao C F, Wang X L, et al. J Biomed Biotech. DOI: 10.1155/2012/985020
23. [23]
  [23] Sköld K, Svensson M, Norrman M, et al. Proteomics, 2007, 7(24): 4445
24. [24]
  [24] Bora A, Annangudi S P, Millet L J, et al. J Proteome Res, 2008, 7(11): 4992
25. [25]
  [25] Sturm R M, Greer T, Woodards N, et al. J Proteome Res, 2013, 12(2): 743
26. [26]
  [26] Svensson M, Sköld K, Svenningsson P, et al. J Proteome Res, 2003, 2(2): 213
27. [27]
  [27] Sköld K, Svensson M, Kaplan A, et al. Proteomics, 2002, 2(4): 447
28. [28]
  [28] Che F Y, Zhang X, Berezniuk I, et al. J Proteome Res, 2007, 6(12): 4667
29. [29]
  [29] Romanova E V, Rubakhin S S, Sweedler J V. Anal Chem, 2008, 80(9): 3379
30. [30]
  [30] Harper R G, Workman S R, Schuetzner S, et al. Electrophoresis, 2004, 25(9): 1299
31. [31]
  [31] Zheng X, Baker H, Hancock W S. J Chromatogr A, 2006, 1120(1/2): 173http://www.northeastern.edu/barnett/faculty/bios/hancock.html
32. [32]
  [32] Greening D W, Simpon R J. J Proteomics, 2010, 73(3): 637
33. [33]
  [33] Zougman A, Pilch B, Podtelejnikov A, et al. J Proteome Res, 2008, 7(1): 386
34. [34]
  [34] Yin P, Knolhoff A M, Rosenberg H J, et al. J Proteome Res, 2012, 11(8): 3965
35. [35]
  [35] Lee J E, Atkins N Jr, Hatcher N G, et al. Mol Cell Proteomics, 2010, 9(2): 285
36. [36]
  [36] Alpert A J, Shukla A K. J Biomol Techniques, 2003, 14: 55
37. [37]
  [37] Kay R, Barton C, Ratcliffe L, et al. Rapid Commun Mass Spectrom, 2008, 22(20): 3255
38. [38]
  [38] Tucholska M, Scozzaro S, Williams D, et al. Anal Biochem, 2007, 370(2): 228
39. [39]
  [39] Polson C, Sarkar P, Incledon B, et al. J Chromatogr B, 2003, 785(2): 263
40. [40]
  [40] Chertov O, Biragyn A, Kwak L W, et al. Proteomics, 2004, 4(4): 1195
41. [41]
  [41] Hayakawa E, Landuyt B, Baggerman G, et al. Peptides, 2013, 42: 63
42. [42]
  [42] Zhao L S, Li Q, Yang W, et al. Chinese Journal of Chromatography (赵龙山, 李清, 杨威, 等. 色谱), 2012, 30(7): 705
43. [43]
  [43] Kawashima Y, Fukutomi T, Tomonaga T, et al. J Proteome Res, 2010, 9(4): 1694
44. [44]
  [44] Vitorino R, Barros A S, Caseiro A, et al. Talanta, 2012, 94: 209
45. [45]
  [45] Potier D N, Griffiths J R, Unwin R D, et al. Anal Chem, 2012, 84(13): 5604
46. [46]
  [46] Engwegen J Y M N, Gast M C W, Schellens J H M, et al. Trends Pharmacol Sci, 2006, 27(5): 251
47. [47]
  [47] Drake R R, Cazares L H, Semmes O J, et al. Expert Rev Mol Diagn, 2005, 5(1): 93
48. [48]
  [48] Zhang Z, Bast R C Jr, Yu Y, et al. Cancer Res, 2004, 64(16): 5882
49. [49]
  [49] Peng J, Stanley A J, Cairns D, et al. Proteomics, 2009, 9(2): 492
50. [50]
  [50] Winder A W J, Gast M C W, Beijnen J H, et al. BMC Medical Genomics, 2009, 2: 4
51. [51]
  [51] Villanueva J, Philip J, Entenberg D, et al. Anal Chem, 2004, 76(6): 1560
52. [52]
  [52] Tiss A, Smith C, Camuzeaux S, et al. Proteomics, 2007, 7(1): 77
53. [53]
  [53] Baumann S, Ceglarek U, Fiedler G M, et al. Clin Chem, 2005, 51(6): 973
54. [54]
  [54] Fiedler G M, Baumann S, Leichtle A, et al. Clin Chem, 2007, 53(3): 421
55. [55]
  [55] Gatlin C L, White K Y, Tracy M B, et al. J Mass Spectrom, 2011, 46(1): 85
56. [56]
  [56] Chen H, Deng C, Li Y, et al. Adv Mater, 2009, 21(21): 2200
57. [57]
  [57] Chen H, Qi D, Deng C, et al. Proteomics, 2009, 9(2): 380
58. [58]
  [58] Chen H, Liu S, Li Y, et al. Proteomics, 2011, 11(5): 890
59. [59]
  [59] Wu C X, Wang C, Wang Z. Chinese Journal of Chromatography (武春霞, 王春, 王志. 色谱), 2011, 29(1): 6
60. [60]
  [60] Li X, Xu S, Pan C, et al. J Sep Sci, 2007, 30(6): 930
61. [61]
  [61] Vallant R M, Szabo Z, Trojer L, et al. J Proteome Res, 2007, 6(1): 44
62. [62]
  [62] Wei L, Shen Q, Lu H, et al. J Chromatogr B, 2009, 877(29): 3631
63. [63]
  [63] Yin P, Zhao M, Deng C. Nanoscale, 2012, 4(22): 6948
64. [64]
  [64] Tian R, Zhang H, Ye M, et al. Angew Chem Int Ed, 2007, 46(6): 962
65. [65]
  [65] Tian R, Ye M, Hu L, et al. J Sep Sci, 2007, 30(14): 2204
66. [66]
  [66] Qin H, Gao P, Wang F, et al. Angew Chem Int Ed, 2011, 50(51): 12218
67. [67]
  [67] Terracciano R, Preianò M, Palladino G P, et al. Proteomics, 2011, 11(16): 3402
68. [68]
  [68] Qian K, Gu W, Yuan P, et al. Small, 2012, 8(2): 231
69. [69]
  [69] Preianò M, Pasqua L, Gallelli L, et al. Proteomics, 2012, 12(22): 3286
70. [70]
  [70] Yin P, Wang Y, Li Y, et al. Proteomics, 2012, 12(18): 2784
71. [71]
  [71] Chen H, Liu S, Yang H, et al. Proteomics, 2010, 10(5): 930
72. [72]
  [72] Liu S, Chen H, Lu X, et al. Angew Chem, 2010, 122(41): 7719
73. [73]
  [73] Wan J, Qian K, Zhang J, et al. Langmuir, 2010, 26(10): 7444
74. [74]
  [74] Zhu G T, Li X S, Fu X M, et al. Chem Commun, 2012, 48(80): 9980
75. [75]
  [75] Hu Y, Bouamrani A, Tasciotti E, et al. ACS Nano, 2010, 4(1): 439
76. [76]
  [76] Tan J, Zhao W J, Yu J K, et al. Adv Healthcare Mater, 2012, 1: 742
77. [77]
  [77] Sudhir P R, Wu H F, Zhou Z C. Anal Chem, 2005, 77(22): 7380
78. [78]
  [78] Gu Z Y, Chen Y J, Jiang J Q, et al. Chem Commun, 2011, 47(16): 4787
79. [79]
  [79] Rodthongkum N, Chen Y, Thayumanavan S, et al. Anal Chem, 2010, 82(20): 8686
80. [80]
  [80] Wu X Y, Wang R, Xie H, et al. Chinese Journal of Chromatography (武晓玉, 王荣, 谢华, 等. 色谱), 2012, 30(8): 810
81. [81]
  [81] Wagner K, Miliotis T, Marko-Varga G, et al. Anal Chem, 2002, 74(4): 809
82. [82]
  [82] Hu L, Boos K S, Ye M, et al. J Chromatogr A, 2009, 1216: 5377
83. [83]
  [83] Luchini A, Geho D H, Bishop B, et al. Nano Lett, 2008, 8(1): 350
84. [84]
  [84] Longo C, Patanarut A, George T, et al. PLoS ONE, 2004, 4(3): e4763
85. [85]
  [85] Fedolini C, Meani F, Reeder K A, et al. Nano Res, 2008, 1(16): 502
86. [86]
  [86] Rainczuk A, Meehan K, Steer D L, et al. Proteomics, 2010, 10(2): 332
87. [87]
  [87] Tamburro D, Fredolini C, Espina V, et al. J Am Chem Soc, 2011, 133(47): 19178
88. [88]
  [88] Tian R, Ren L, Ma H, et al. J Chromatogr A, 2009, 1216: 1270
89. [89]
  [89] Hu L, Zhou H, Li Y, et al. Anal Chem, 2009, 81(1): 94
90. [90]
  [90] Zhu J, Wang F, Cheng K, et al. J Proteomics, 2013, 78: 389
91. [91]
  [91] Liu L, Zhang Y, Zhang L, et al. Anal Chim Acta, 2012, 753: 64
92. [92]
  [92] Hu L, Li X, Jiang X, et al. J Proteome Res, 2007, 6(2): 801
93. [93]
  [93] Shen Y, Liu T, Tolić N, et al. J Proteome Res, 2010, 9(5): 2339
94. [94]
  [94] Ly L, Wasinger V C. Proteomics, 2008, 8(20): 4197
95. [95]
  [95] Kamphorst J J, Tjaden U R, Heijden R, et al. Electrophoresis, 2009, 30(13): 2284
96. [96]
  [96] Tanaka K, Tsugawa N, Kim Y O, et al. Biochem Biophys Res Commun, 2009, 379(1): 110
1. [1]
  Xinyi Hong , Tailing Xue , Zhou Xu , Enrong Xie , Mingkai Wu , Qingqing Wang , Lina Wu . Non-Site-Specific Fluorescent Labeling of Proteins as a Chemical Biology Experiment. University Chemistry, 2024, 39(4): 351-360. doi: 10.3866/PKU.DXHX202310010
2. [2]
  Zhi Zheng , Feiyang Liu , Junlong Zhao . D-Amino Acids and Mirror-Image Proteins. University Chemistry, 2026, 41(2): 353-359. doi: 10.12461/PKU.DXHX202505017
3. [3]
  Zihan Lin , Wanzhen Lin , Fa-Jie Chen . Electrochemical Modifications of Native Peptides. University Chemistry, 2025, 40(3): 318-327. doi: 10.12461/PKU.DXHX202406089
4. [4]
  Xinran Zhang , Siqi Liu , Yichi Chen , Qingli Zou , Qinghong Xu , Yaqin Huang . From Protein to Energy Storage Materials: Edible Gelatin Jelly Electrolyte. University Chemistry, 2025, 40(7): 255-266. doi: 10.12461/PKU.DXHX202408104
5. [5]
  Zehua Zhao , Xiaoyan An , Jinrong Xu , Ling Yang , Hao Zhao , Zhongyun Wu . Independent Development and Application of Calorimetric Experiment Data Acquisition and Processing Software. University Chemistry, 2025, 40(11): 402-408. doi: 10.12461/PKU.DXHX202505045
6. [6]
  Pingping Zhu , Qiang Zhou , Yu Huang , Haiyang Yang , Pingsheng He , Shiyan Xiao . Design and Practice of Ideological and Political Cases in the Course of Polymer Physics Experiments: Molecular Weight Determination of Polymers by Dilute Solution Viscosity Method as an Example. University Chemistry, 2025, 40(4): 94-99. doi: 10.12461/PKU.DXHX202405170
7. [7]
  Jin Tong , Shuyan Yu . Crystal Engineering for Supramolecular Chirality. University Chemistry, 2024, 39(3): 86-93. doi: 10.3866/PKU.DXHX202308113
8. [8]
  Zufeng Qiu , Jie Ouyang , Yiru Wang , Hengting Yang , Xin Liao , Chi Zhang , Xuanyao Jiang , Shunliu Deng , Zhiwei Lin . 综合运用分析仪器解析“盲盒”样品——未知物的剖析. University Chemistry, 2025, 40(6): 296-302. doi: 10.12461/PKU.DXHX202405167
9. [9]
  Jing Wang , Pingping Li , Yuehui Wang , Yifan Xiu , Bingqian Zhang , Shuwen Wang , Hongtao Gao . Treatment and Discharge Evaluation of Phosphorus-Containing Wastewater. University Chemistry, 2024, 39(5): 52-62. doi: 10.3866/PKU.DXHX202309097
10. [10]
  Fa Wang , Yu Chen , Hui Chao . Ruthenium(II) Complexes as Photoactivated Chemo-Prodrugs for Hypoxic Tumor Therapy. University Chemistry, 2025, 40(7): 200-212. doi: 10.12461/PKU.DXHX202410024
11. [11]
  Yujing Chen , Hongqun Ouyang , Dan Zhao , Yanyan Chu , Zhengping Qiao . Recommendations for the Content and Instruction of the Physical Chemistry Experiment “Construction of Ternary Liquid-Liquid Phase Diagrams”. University Chemistry, 2025, 40(7): 359-366. doi: 10.12461/PKU.DXHX202409120
12. [12]
  Songmei Ma , Ying Zhang , Gang Liu , Wenlong Xu . Comprehensive Experiment Teaching Exploration and Practice in Polymeric Materials Integrating Research-Driven Learning, Creativity-Enhanced Competency, and Science-Education Synergy: A Case Study of Machine Learning-Assisted Intelligent Handwriting Recognition System. University Chemistry, 2026, 41(1): 289-297. doi: 10.12461/PKU.DXHX202509083
13. [13]
  Zhaohu Li , Weidong Wang , Yuhao Liu , Mingzhe Han , Lingling Wei , Huan Jiao . Research on the Safety Management and Disposal of Chemical Laboratory Waste. University Chemistry, 2024, 39(10): 128-136. doi: 10.3866/PKU.DXHX202312090
14. [14]
  Zhongyan Cao , Shengnan Jin , Yuxia Wang , Yiyi Chen , Xianqiang Kong , Yuanqing Xu . Advances in Highly Selective Reactions Involving Phenol Derivatives as Aryl Radical Precursors. University Chemistry, 2025, 40(4): 245-252. doi: 10.12461/PKU.DXHX202405186
15. [15]
  Qingyu Yang , Yuanhai Yu , Yanliu Wu , Ting Yang , Le Zhong , Wenhong Ruan , Jie Li . Digital Intelligence-Empowered Exploration of Copolymerized Polyacrylonitrile Synthesis and Application Experiments for Carbon Fiber Precursors. University Chemistry, 2026, 41(1): 41-56. doi: 10.12461/PKU.DXHX202506010
16. [16]
  Lisen Sun , Yongmei Hao , Zhen Huang , Yongmei Liu . Experimental Teaching Design for Viscosity Measurement Serves the Optimization of Operating Conditions for Kitchen Waste Treatment Equipment. University Chemistry, 2024, 39(2): 52-56. doi: 10.3866/PKU.DXHX202307063
17. [17]
  Kun Xu , Xinxin Song , Zhilei Yin , Jian Yang , Qisheng Song . Comprehensive Experimental Design of Preferential Orientation of Zinc Metal by Heat Treatment for Enhanced Electrochemical Performance. University Chemistry, 2024, 39(4): 192-197. doi: 10.3866/PKU.DXHX202309050
18. [18]
  Jia Huo , Jia Li , Yongjun Li , Yuzhi Wang . Ideological and Political Design of Physical Chemistry Teaching: Chemical Potential of Any Component in an Ideal-Dilute Solution. University Chemistry, 2024, 39(2): 14-20. doi: 10.3866/PKU.DXHX202307075
19. [19]
  Xianfei Chen , Wentao Zhang , Haiying Du . Experimental Design of Computational Materials Science Based on Scientific Research Cases. University Chemistry, 2025, 40(3): 52-61. doi: 10.3866/PKU.DXHX202403112
20. [20]
  Chunai Dai , Yongsheng Han , Luting Yan , Zhen Li , Yingze Cao . Preparation of Superhydrophobic Surfaces and Their Application in Oily Wastewater Treatment: Design of a Comprehensive Physical Chemistry Innovation Experiment. University Chemistry, 2024, 39(2): 34-40. doi: 10.3866/PKU.DXHX202307081

Get Citation

PDF

XML

Metrics

PDF Downloads(0)
Abstract views(1057)
HTML views(283)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142