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Journal of Biomedicine and Biotechnology
Volume 2011, Article ID 245291, 14 pages
http://dx.doi.org/10.1155/2011/245291
Review Article

Sample Preparation Techniques for the Untargeted LC-MS-Based Discovery of Peptides in Complex Biological Matrices

1Laboratory for Analytical Biotechnology and Innovative Peptide Biology, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 3706 AV Zeist, The Netherlands
2Netherlands Proteomics Centre, Delft University of Technology, Julianalaan 67, 3706 AV Zeist, The Netherlands
3TNO Triskelion, 3700 AV Zeist, The Netherlands
4Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium

Received 16 June 2011; Accepted 1 September 2011

Academic Editor: Isabel Sá-Correia

Copyright © 2011 Inez Finoulst et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. M. Schrader and P. Schulz-Knappe, “Peptidomics technologies for human body fluids,” Trends in Biotechnology, vol. 19, supplement 10, pp. S55–S60, 2001. View at Google Scholar · View at Scopus
  2. L. Hu, M. Ye, and H. Zou, “Recent advances in mass spectrometry-based peptidome analysis,” Expert Review of Proteomics, vol. 6, no. 4, pp. 433–447, 2009. View at Publisher · View at Google Scholar · View at Scopus
  3. C. R. Jimenez, S. Piersma, and T. V. Pham, “High-throughput and targeted in-depth mass spectrometry-based approaches for biofluid profiling and biomarker discovery,” Biomarkers in Medicine, vol. 1, no. 4, pp. 541–565, 2007. View at Google Scholar
  4. X. Jiang, M. Ye, and H. Zou, “Technologies and methods for sample pretreatment in efficient proteome and peptidome analysis,” Proteomics, vol. 8, no. 4, pp. 686–705, 2008. View at Publisher · View at Google Scholar · View at Scopus
  5. P. Schulz-Knappe, H. D. Zucht, G. Heine, M. Jürgens, R. Hess, and M. Schrader, “Peptidomics: the comprehensive analysis of peptides in complex biological mixtures,” Combinatorial Chemistry and High Throughput Screening, vol. 4, no. 2, pp. 207–217, 2001. View at Google Scholar · View at Scopus
  6. A. D. McNaught and A. Wilkinson, Eds., Compendium of Chemical Terminology—The Gold Book, Second Edition, Blackwell Science, 2nd edition, 1997.
  7. J. S. Gelman, J. Sironi, L. M. Castro, E. S. Ferro, and L. D. Fricker, “Peptidomic analysis of human cell lines,” Journal of Proteome Research, vol. 10, no. 4, pp. 1583–1592, 2011. View at Publisher · View at Google Scholar
  8. M. Soloviev and P. Finch, “Peptidomics: bridging the gap between proteome and metabolome,” Proteomics, vol. 6, no. 3, pp. 744–747, 2006. View at Publisher · View at Google Scholar · View at Scopus
  9. Y. Hathout, “Approaches to the study of the cell secretome,” Expert Review of Proteomics, vol. 4, no. 2, pp. 239–248, 2007. View at Publisher · View at Google Scholar · View at Scopus
  10. X. Liang, J. Huuskonen, M. Hajivandi et al., “Identification and quantification of proteins differentially secreted by a pair of normal and malignant breast-cancer cell lines,” Proteomics, vol. 9, no. 1, pp. 182–193, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. M. Makridakis and A. Vlahou, “Secretome proteomics for discovery of cancer biomarkers,” Journal of Proteomics, vol. 73, no. 12, pp. 2291–2305, 2010. View at Publisher · View at Google Scholar · View at Scopus
  12. B. Domon and R. Aebersold, “Options and considerations when selecting a quantitative proteomics strategy,” Nature Biotechnology, vol. 28, no. 7, pp. 710–721, 2010. View at Publisher · View at Google Scholar · View at Scopus
  13. M. S. Kim, K. Kandasamy, R. Chaerkady, and A. Pandey, “Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-orbitrap mass spectrometer,” Journal of the American Society for Mass Spectrometry, vol. 21, no. 9, pp. 1606–1611, 2010. View at Publisher · View at Google Scholar · View at Scopus
  14. T. Nilsson, M. Mann, R. Aebersold, J. R. Yates, A. Bairoch, and J. J. M. Bergeron, “Mass spectrometry in high-throughput proteomics: ready for the big time,” Nature Methods, vol. 7, no. 9, pp. 681–685, 2010. View at Publisher · View at Google Scholar · View at Scopus
  15. K. Ueda, N. Saichi, S. Takami et al., “A comprehensive peptidome profiling technology for the identification of early detection biomarkers for lung adenocarcinoma,” PLoS One, vol. 6, no. 4, Article ID e18567, 2011. View at Publisher · View at Google Scholar
  16. T. Liu, W. J. Qian, H. M. Mottaz et al., “Evaluation of multiprotein immunoaffnity subtraction for plasma proteomics and candidate biomaker discovery using mass spectrometry,” Molecular and Cellular Proteomics, vol. 5, no. 11, pp. 2167–2174, 2006. View at Publisher · View at Google Scholar · View at Scopus
  17. J. L. Richens, E. A. M. Lunt, D. Sanger, G. McKenzie, and P. O'Shea, “Avoiding nonspecific interactions in studies of the plasma proteome: practical solutions to prevention of nonspecific interactions for label-free detection of low-abundance plasma proteins,” Journal of Proteome Research, vol. 8, no. 11, pp. 5103–5110, 2009. View at Publisher · View at Google Scholar · View at Scopus
  18. M. Makridakis, M. G. Roubelakis, V. Bitsika et al., “Analysis of secreted proteins for the study of bladder cancer cell aggressiveness,” Journal of Proteome Research, vol. 9, no. 6, pp. 3243–3259, 2010. View at Publisher · View at Google Scholar · View at Scopus
  19. X. Zhang, A. Fang, C. P. Riley, M. Wang, F. E. Regnier, and C. Buck, “Multi-dimensional liquid chromatography in proteomics-A review,” Analytica Chimica Acta, vol. 664, no. 2, pp. 101–113, 2010. View at Publisher · View at Google Scholar · View at Scopus
  20. R. S. Tirumalai, K. C. Chan, D. A. Prieto, H. J. Issaq, T. P. Conrads, and T. D. Veenstra, “Characterization of the low molecular weight human serum proteome,” Molecular & Cellular Proteomics, vol. 2, no. 10, pp. 1096–1103, 2003. View at Google Scholar · View at Scopus
  21. N. L. Anderson and N. G. Anderson, “The human plasma proteome: history, character, and diagnostic prospects,” Molecular & Cellular Proteomics, vol. 1, no. 11, pp. 845–867, 2002. View at Google Scholar · View at Scopus
  22. X. Fang and W. W. Zhang, “Affinity separation and enrichment methods in proteomic analysis,” Journal of Proteomics, vol. 71, no. 3, pp. 284–303, 2008. View at Publisher · View at Google Scholar · View at Scopus
  23. P. Hernandez, M. Müller, and R. D. Appel, “Automated protein identification by tandem mass spectrumetry: issues and strategies,” Mass Spectrometry Reviews, vol. 25, no. 2, pp. 235–254, 2006. View at Publisher · View at Google Scholar · View at Scopus
  24. B. Shushan, “A review of clinical diagnostic applications of liquid chromatography- tandem mass spectrometry,” Mass Spectrometry Reviews, vol. 29, no. 6, pp. 930–944, 2010. View at Publisher · View at Google Scholar · View at Scopus
  25. H. Mirzaei and F. Regnier, “Structure specific chromatographic selection in targeted proteomics,” Journal of Chromatography B, vol. 817, no. 1, pp. 23–34, 2005. View at Publisher · View at Google Scholar
  26. J. Hernández-Borges, T. M. Borges-Miquel, M. A. Rodríguez-Delgado, and A. Cifuentes, “Sample treatments prior to capillary electrophoresis-mass spectrometry,” Journal of Chromatography A, vol. 1153, no. 1-2, pp. 214–226, 2007. View at Publisher · View at Google Scholar · View at Scopus
  27. C. Planque, V. Kulasingam, C. R. Smith, K. Reckamp, L. Goodglick, and E. P. Diamandis, “Identification of five candidate lung cancer biomarkers by proteomics analysis of conditioned media of four lung cancer cell lines,” Molecular and Cellular Proteomics, vol. 8, no. 12, pp. 2746–2758, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. M. Chevallet, H. Diemer, A. Van Dorssealer, C. Villiers, and T. Rabilloud, “Toward a better analysis of secreted proteins: the example of the myeloid cells secretome,” Proteomics, vol. 7, no. 11, pp. 1757–1770, 2007. View at Publisher · View at Google Scholar · View at Scopus
  29. M. Colzani, P. Waridel, J. Laurent, E. Faes, C. Rüegg, and M. Quadroni, “Metabolic labeling and protein linearization technology allow the study of proteins secreted by cultured cells in serum-containing media,” Journal of Proteome Research, vol. 8, no. 10, pp. 4779–4788, 2009. View at Publisher · View at Google Scholar · View at Scopus
  30. P. Dowling and M. Clynes, “Conditioned media from cell lines: a complementary model to clinical specimens for the discovery of disease-specific biomarkers,” Proteomics, vol. 11, no. 4, pp. 794–804, 2011. View at Publisher · View at Google Scholar
  31. T. M. Greco, S. H. Seeholzer, A. Mak, L. Spruce, and H. Ischiropoulos, “Quantitative mass spectrometry-based proteomics reveals the dynamic range of primary mouse astrocyte protein secretion,” Journal of Proteome Research, vol. 9, no. 5, pp. 2764–2774, 2010. View at Publisher · View at Google Scholar · View at Scopus
  32. J. F. Peter, A. M. Otto, and B. Wolf, “Enrichment and detection of molecules secreted by tumor cells using magnetic reversed-phase particles and LC-MALDI-TOF-MS,” Journal of Biomolecular Techniques, vol. 18, no. 5, pp. 287–297, 2007. View at Google Scholar · View at Scopus
  33. K. Sintiprungrat, N. Singhto, S. Sinchaikul, S. T. Chen, and V. Thongboonkerd, “Alterations in cellular proteome and secretome upon differentiation from monocyte to macrophage by treatment with phorbol myristate acetate: insights into biological processes,” Journal of Proteomics, vol. 73, no. 3, pp. 602–618, 2010. View at Publisher · View at Google Scholar · View at Scopus
  34. B. J. Xu, W. Yan, B. Jovanovic et al., “Quantitative analysis of the secretome of TGF-β signaling-deficient mammary fibroblasts,” Proteomics, vol. 10, no. 13, pp. 2458–2470, 2010. View at Publisher · View at Google Scholar · View at Scopus
  35. L. Alldridge, G. Metodieva, C. Greenwood et al., “Proteome profiling of breast tumors by gel electrophoresis and nanoscale electrospray ionization mass spectrometry,” Journal of Proteome Research, vol. 7, no. 4, pp. 1458–1469, 2008. View at Publisher · View at Google Scholar · View at Scopus
  36. D. E. Garfin, “One-dimensional gel electrophoresis,” Methods in Enzymology, vol. 463, pp. 497–513, 2009. View at Publisher · View at Google Scholar · View at Scopus
  37. J. Moebiust, R. P. Zahedi, U. Lewandrowski, C. Berger, U. Walter, and A. Sickmann, “The human platelet membrane proteome reveals several new potential membrane proteins,” Molecular and Cellular Proteomics, vol. 4, no. 11, pp. 1754–1761, 2005. View at Publisher · View at Google Scholar · View at Scopus
  38. A. Shevchenko, H. Tomas, J. Havliš, J. V. Olsen, and M. Mann, “In-gel digestion for mass spectrometric characterization of proteins and proteomes,” Nature Protocols, vol. 1, no. 6, pp. 2856–2860, 2006. View at Publisher · View at Google Scholar · View at Scopus
  39. L. Wu and D. K. Han, “Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics,” Expert Review of Proteomics, vol. 3, no. 6, pp. 611–619, 2006. View at Publisher · View at Google Scholar · View at Scopus
  40. G. Zhang, D. Fenyö, and T. A. Neubert, “Use of DNA ladders for reproducible protein fractionation by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) for quantitative proteomics,” Journal of Proteome Research, vol. 7, no. 2, pp. 678–686, 2008. View at Publisher · View at Google Scholar · View at Scopus
  41. G. M. Walsh, J. C. Rogalski, C. Klockenbusch, and J. Kast, “Mass spectrometry-based proteomics in biomedical research: emerging technologies and future strategies,” Expert Reviews in Molecular Medicine, vol. 12, p. e30, 2010. View at Google Scholar
  42. D. B. Friedman, S. Hoving, and R. Westermeier, “Isoelectric focusing and two-dimensional gel electrophoresis,” Methods in Enzymology, vol. 463, pp. 515–540, 2009. View at Publisher · View at Google Scholar · View at Scopus
  43. H. Liu, D. Lin, and J. R. Yates III, “Multidimensional separations for protein/peptide analysis in the post-genomic era,” BioTechniques, vol. 32, no. 4, pp. 898–902, 2002. View at Google Scholar
  44. L. Ly and V. C. Wasinger, “Protein and peptide fractionation, enrichment and depletion: tools for the complex proteome,” Proteomics, vol. 11, no. 4, pp. 513–534, 2011. View at Publisher · View at Google Scholar
  45. T. Rabilloud, “Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains,” Proteomics, vol. 2, no. 1, pp. 3–10, 2002. View at Publisher · View at Google Scholar · View at Scopus
  46. M. Schirle, M. A. Heurtier, and B. Kuster, “Profiling core proteomes of human cell lines by one-dimensional PAGE and liquid chromatography-tandem mass spectrometry,” Molecular & Cellular Proteomics, vol. 2, no. 12, pp. 1297–1305, 2003. View at Google Scholar · View at Scopus
  47. F. Chevalier, “Highlights on the capacities of 'Gel-based' proteomics,” Proteome Science, vol. 8, article no. 23, 2010. View at Publisher · View at Google Scholar · View at Scopus
  48. B. Granvogl, M. Plöscher, and L. A. Eichacker, “Sample preparation by in-gel digestion for mass spectrometry-based proteomics,” Analytical and Bioanalytical Chemistry, vol. 389, no. 4, pp. 991–1002, 2007. View at Publisher · View at Google Scholar · View at Scopus
  49. I. Miller, J. Crawford, and E. Gianazza, “Protein stains for proteomic applications: which, when, why?” Proteomics, vol. 6, no. 20, pp. 5385–5408, 2006. View at Publisher · View at Google Scholar · View at Scopus
  50. T. H. Steinberg, “Protein gel staining methods. An introduction and overview,” Methods in Enzymology, vol. 463, pp. 541–563, 2009. View at Publisher · View at Google Scholar · View at Scopus
  51. F. E. Ahmed, “Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry,” Journal of Separation Science, vol. 32, no. 5-6, pp. 771–798, 2009. View at Publisher · View at Google Scholar · View at Scopus
  52. S. M. Cologna, W. K. Russell, P. J. Lim, G. Vigh, and D. H. Russell, “Combining isoelectric point-based fractionation, liquid chromatography and mass spectrometry to improve peptide detection and protein identification,” Journal of the American Society for Mass Spectrometry, vol. 21, no. 9, pp. 1612–1619, 2010. View at Publisher · View at Google Scholar · View at Scopus
  53. A. Ros, M. Faupel, H. Mees et al., “Protein purification by off-gel electrophoresis,” Proteomics, vol. 2, no. 2, pp. 151–156, 2002. View at Publisher · View at Google Scholar · View at Scopus
  54. N. C. Hubner, S. Ren, and M. Mann, “Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis,” Proteomics, vol. 8, no. 23-24, pp. 4862–4872, 2008. View at Publisher · View at Google Scholar · View at Scopus
  55. B. Manadas, J. A. English, K. J. Wynne, D. R. Cotter, and M. J. Dunn, “Comparative analysis of OFFGel, strong cation exchange with pH gradient, and RP at high pH for first-dimensional separation of peptides from a membrane-enriched protein fraction,” Proteomics, vol. 9, no. 22, pp. 5194–5198, 2009. View at Publisher · View at Google Scholar · View at Scopus
  56. J. N. Adkins, S. M. Varnum, K. J. Auberry et al., “Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry,” Molecular & Cellular Proteomics, vol. 1, no. 12, pp. 947–955, 2002. View at Google Scholar · View at Scopus
  57. T. Baussant, L. Bougueleret, A. Johnson et al., “Effective depletion of albumin using a new peptide-based affinity medium,” Proteomics, vol. 5, no. 4, pp. 973–977, 2005. View at Publisher · View at Google Scholar · View at Scopus
  58. Y. Gong, X. Li, B. Yang et al., “Different immunoaffinity fractionation strategies to characterize the human plasma proteome,” Journal of Proteome Research, vol. 5, no. 6, pp. 1379–1387, 2006. View at Publisher · View at Google Scholar · View at Scopus
  59. J. Granger, J. Siddiqui, S. Copeland, and D. Remick, “Albumin depletion of human plasma also removes low abundance proteins including the cytokines,” Proteomics, vol. 5, no. 18, pp. 4713–4718, 2005. View at Publisher · View at Google Scholar · View at Scopus
  60. S. Roche, L. Tiers, M. Provansal et al., “Depletion of one, six, twelve or twenty major blood proteins before proteomic analysis: the more the better?” Journal of Proteomics, vol. 72, no. 6, pp. 945–951, 2009. View at Publisher · View at Google Scholar · View at Scopus
  61. M. Urh, D. Simpson, and K. Zhao, “Affinity chromatography. General methods,” Methods in Enzymology, vol. 463, pp. 417–438, 2009. View at Publisher · View at Google Scholar · View at Scopus
  62. N. Zolotarjova, J. Martosella, G. Nicol, J. Bailey, B. E. Boyes, and W. C. Barrett, “Differences among techniques for high-abundant protein depletion,” Proteomics, vol. 5, no. 13, pp. 3304–3313, 2005. View at Publisher · View at Google Scholar · View at Scopus
  63. M. Zhou, D. A. Lucas, K. C. Chan et al., “An investigation into the human serum "interactome",” Electrophoresis, vol. 25, no. 9, pp. 1289–1298, 2004. View at Publisher · View at Google Scholar · View at Scopus
  64. S. R. Gallant, V. Koppaka, and N. Zecherle, “Dye ligand chromatography,” Methods in Molecular Biology, vol. 421, pp. 61–69, 2008. View at Google Scholar · View at Scopus
  65. L. A. Echan, H. Y. Tang, N. Ali-Khan, K. Lee, and D. W. Speicher, “Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma,” Proteomics, vol. 5, no. 13, pp. 3292–3303, 2005. View at Publisher · View at Google Scholar · View at Scopus
  66. G. Maccarrone, D. Milfay, I. Birg et al., “Mining the human cerebrospinal fluid proteome by immunodepletion and shotgun mass spectrometry,” Electrophoresis, vol. 25, no. 14, pp. 2402–2412, 2004. View at Publisher · View at Google Scholar · View at Scopus
  67. C. Tu, P. A. Rudnick, M. Y. Martinez et al., “Depletion of abundant plasma proteins and limitations of plasma proteomics,” Journal of Proteome Research, vol. 9, no. 10, pp. 4982–4991, 2010. View at Publisher · View at Google Scholar · View at Scopus
  68. H. Ye, L. Sun, X. Huang, P. Zhang, and X. Zhao, “A proteomic approach for plasma biomarker discovery with 8-plex iTRAQ labeling and SCX-LC-MS/MS,” Molecular and Cellular Biochemistry, vol. 343, no. 1-2, pp. 91–99, 2010. View at Publisher · View at Google Scholar · View at Scopus
  69. P. G. Righetti, E. Boschetti, L. Lomas, and A. Citterio, “Protein Equalizer Technology : the quest for a "democratic proteome",” Proteomics, vol. 6, no. 14, pp. 3980–3992, 2006. View at Publisher · View at Google Scholar · View at Scopus
  70. E. M. Keidel, D. Ribitsch, and F. Lottspeich, “Equalizer technology—equal rights for disparate beads,” Proteomics, vol. 10, no. 11, pp. 2089–2098, 2010. View at Publisher · View at Google Scholar · View at Scopus
  71. V. Polaskova, A. Kapur, A. Khan, M. P. Molloy, and M. S. Baker, “High-abundance protein depletion: comparison of methods for human plasma biomarker discovery,” Electrophoresis, vol. 31, no. 3, pp. 471–482, 2010. View at Publisher · View at Google Scholar · View at Scopus
  72. R. E. Hansen and J. R. Winther, “An introduction to methods for analyzing thiols and disulfides: reactions, reagents, and practical considerations,” Analytical Biochemistry, vol. 394, no. 2, pp. 147–158, 2009. View at Publisher · View at Google Scholar · View at Scopus
  73. A. C. Grabski, “Advances in preparation of biological extracts for protein purification,” Methods in Enzymology, vol. 463, pp. 285–303, 2009. View at Publisher · View at Google Scholar · View at Scopus
  74. H. Řehulková, M. Marchetti-Deschmann, E. Pittenauer, G. Allmaier, and P. Řehulka, “Improved identification of hordeins by cysteine alkylation with 2-bromoethylamine, SDS-PAGE and subsequent in-gel tryptic digestion,” Journal of Mass Spectrometry, vol. 44, no. 11, pp. 1613–1621, 2009. View at Publisher · View at Google Scholar · View at Scopus
  75. M. Thevis, R. R. Ogorzalek Loo, and J. A. Loo, “In-gel derivatization of proteins for cysteine-specific cleavages and their analysis by mass spectrometry,” Journal of Proteome Research, vol. 2, no. 2, pp. 163–172, 2003. View at Publisher · View at Google Scholar · View at Scopus
  76. J. V. Olsen, S. E. Ong, and M. Mann, “Trypsin cleaves exclusively C-terminal to arginine and lysine residues,” Molecular and Cellular Proteomics, vol. 3, no. 6, pp. 608–614, 2004. View at Publisher · View at Google Scholar · View at Scopus
  77. M. A. Baldwin, “Protein identification by mass spectrometry: issues to be considered,” Molecular and Cellular Proteomics, vol. 3, no. 1, pp. 1–9, 2004. View at Publisher · View at Google Scholar · View at Scopus
  78. J. V. Olsen, L. M. F. de Godoy, G. Li et al., “Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a C-trap,” Molecular and Cellular Proteomics, vol. 4, no. 12, pp. 2010–2021, 2005. View at Publisher · View at Google Scholar · View at Scopus
  79. L. M. de Godoy, J. V. Olsen, G. A. de Souza, G. Li, P. Mortensen, and M. Mann, “Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system,” Genome Biology, vol. 7, no. 6, article R50, 2006. View at Publisher · View at Google Scholar · View at Scopus
  80. A. Scholten, S. Mohammed, T. Y. Low et al., “In-depth quantitative cardiac proteomics combining electron transfer dissociation and the metalloendopeptidase Lys-N with the SILAC mouse,” Molecular & Cellular Proteomics. In press. View at Publisher · View at Google Scholar
  81. A. Zougman, B. Pilch, A. Podtelejnikov et al., “Integrated analysis of the cerebrospinal fluid peptidome and proteome,” Journal of Proteome Research, vol. 7, no. 1, pp. 386–399, 2008. View at Publisher · View at Google Scholar · View at Scopus
  82. M. Tucholska, S. Scozzaro, D. Williams et al., “Endogenous peptides from biophysical and biochemical fractionation of serum analyzed by matrix-assisted laser desorption/ionization and electrospray ionization hybrid quadrupole time-of-flight,” Analytical Biochemistry, vol. 370, no. 2, pp. 228–245, 2007. View at Publisher · View at Google Scholar · View at Scopus
  83. X. Zheng, H. Baker, and W. S. Hancock, “Analysis of the low molecular weight serum peptidome using ultrafiltration and a hybrid ion trap-Fourier transform mass spectrometer,” Journal of Chromatography A, vol. 1120, no. 1-2, pp. 173–184, 2006. View at Publisher · View at Google Scholar · View at Scopus
  84. E. Orvisky, S. K. Drake, B. M. Martin et al., “Enrichment of low molecular weight fraction of serum for MS analysis of peptides associated with hepatocellular carcinoma,” Proteomics, vol. 6, no. 9, pp. 2895–2902, 2006. View at Publisher · View at Google Scholar · View at Scopus
  85. K. Merrell, K. Southwick, S. W. Graves, M. S. Esplin, N. E. Lewis, and C. D. Thulin, “Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometry,” Journal of Biomolecular Techniques, vol. 15, no. 4, pp. 238–248, 2004. View at Google Scholar · View at Scopus
  86. R. G. Harper, S. R. Workman, S. Schuetzner, A. T. Timperman, and J. N. Sutton, “Low-molecular-weight human serum proteome using ultrafiltration, isoelectric focusing, and mass spectrometry,” Electrophoresis, vol. 25, no. 9, pp. 1299–1306, 2004. View at Publisher · View at Google Scholar · View at Scopus
  87. D. W. Greening and R. J. Simpson, “A centrifugal ultrafiltration strategy for isolating the low-molecular weight (<or=25 K) component of human plasma proteome,” Journal of Proteomics, vol. 73, no. 3, pp. 637–648, 2010. View at Publisher · View at Google Scholar · View at Scopus
  88. J. R. Wiśniewski, D. F. Zielinska, and M. Mann, “Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method,” Analytical Biochemistry, vol. 410, no. 2, pp. 307–309, 2011. View at Publisher · View at Google Scholar
  89. J. R. Wiśniewski, A. Zougman, N. Nagaraj, and M. Mann, “Universal sample preparation method for proteome analysis,” Nature Methods, vol. 6, no. 5, pp. 359–362, 2009. View at Publisher · View at Google Scholar · View at Scopus
  90. O. Chertov, A. Biragyn, L. W. Kwak et al., “Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry,” Proteomics, vol. 4, no. 4, pp. 1195–1203, 2004. View at Publisher · View at Google Scholar · View at Scopus
  91. R. Kay, C. Barton, L. Ratcliffe et al., “Enrichment of low molecular weight serum proteins using acetonitrile precipitation for mass spectrometry based proteomic analysis,” Rapid Communications in Mass Spectrometry, vol. 22, no. 20, pp. 3255–3260, 2008. View at Publisher · View at Google Scholar · View at Scopus
  92. D. Williams, S. Ackloo, P. Zhu et al., “Precipitation and selective extraction of human serum endogenous peptides with analysis by quadrupole time-of-flight mass spectrometry reveals posttranslational modifications and low-abundance peptides,” Analytical and Bioanalytical Chemistry, vol. 396, no. 3, pp. 1223–1247, 2010. View at Publisher · View at Google Scholar · View at Scopus
  93. C. Polson, P. Sarkar, B. Incledon, V. Raguvaran, and R. Grant, “Optimization of protein precipitation based upon effectiveness of protein removal and ionization effect in liquid chromatography-tandem mass spectrometry,” Journal of Chromatography B, vol. 785, no. 2, pp. 263–275, 2003. View at Publisher · View at Google Scholar
  94. Y. Kawashima, T. Fukutomi, T. Tomonaga et al., “High-yield peptide-extraction method for the discovery of subnanomolar biomarkers from small serum samples,” Journal of Proteome Research, vol. 9, no. 4, pp. 1694–1705, 2010. View at Publisher · View at Google Scholar · View at Scopus
  95. J. Albrethsen, R. Bøgebo, S. Gammeltoft, J. Olsen, B. Winther, and H. Raskov, “Upregulated expression of human neutrophil peptides 1,2 and 3 (HNP 1–3) in colon cancer serum and tumours: a biomarker study,” BMC Cancer, vol. 5, article 8, 2005. View at Publisher · View at Google Scholar · View at Scopus
  96. K. Sasaki, N. Takahashi, M. Satoh, M. Yamasaki, and N. Minamino, “A peptidomics strategy for discovering endogenous bioactive peptides,” Journal of Proteome Research, vol. 9, no. 10, pp. 5047–5052, 2010. View at Publisher · View at Google Scholar · View at Scopus
  97. L. Hu, X. Li, X. Jiang et al., “Comprehensive peptidome analysis of mouse livers by size exclusion chromatography prefractionation and nanoLC-MS/MS identification,” Journal of Proteome Research, vol. 6, no. 2, pp. 801–808, 2007. View at Publisher · View at Google Scholar · View at Scopus
  98. A. Makarov and M. Scigelova, “Coupling liquid chromatography to Orbitrap mass spectrometry,” Journal of Chromatography A, vol. 1217, no. 25, pp. 3938–3945, 2010. View at Publisher · View at Google Scholar · View at Scopus
  99. M. P. Ebert, D. Niemeyer, S. O. Deininger et al., “Identification and confirmation of increased fibrinopeptide A serum protein levels in gastric cancer sera by magnet bead assisted MALDI-TOF mass spectrometry,” Journal of Proteome Research, vol. 5, no. 9, pp. 2152–2158, 2006. View at Publisher · View at Google Scholar · View at Scopus
  100. D. Guillarme, J. Ruta, S. Rudaz, and J. L. Veuthey, “New trends in fast and high-resolution liquid chromatography: a critical comparison of existing approaches,” Analytical and Bioanalytical Chemistry, vol. 397, no. 3, pp. 1069–1082, 2010. View at Publisher · View at Google Scholar · View at Scopus
  101. K. Sandra, M. Moshir, F. D'hondt, K. Verleysen, K. Kas, and P. Sandra, “Highly efficient peptide separations in proteomics. Part 1. Unidimensional high performance liquid chromatography,” Journal of Chromatography B, vol. 866, no. 1-2, pp. 48–63, 2008. View at Publisher · View at Google Scholar
  102. W. A. Waterval, J. L. J. M. Scheijen, M. M. J. C. Ortmans-Ploemen, C. D. Habets-van der Poel, and J. Bierau, “Quantitative UPLC-MS/MS analysis of underivatised amino acids in body fluids is a reliable tool for the diagnosis and follow-up of patients with inborn errors of metabolism,” Clinica Chimica Acta, vol. 407, no. 1-2, pp. 36–42, 2009. View at Publisher · View at Google Scholar · View at Scopus
  103. F. T. Peters, “Recent advances of liquid chromatography-(tandem) mass spectrometry in clinical and forensic toxicology,” Clinical Biochemistry, vol. 44, no. 1, pp. 54–65, 2011. View at Publisher · View at Google Scholar · View at Scopus
  104. K. Sköld, M. Svensson, M. Norrman, B. Sjögren, P. Svenningsson, and P. E. Andrén, “The significance of biochemical and molecular sample integrity in brain proteomics and peptidomics: stathmin 2-20 and peptides as sample quality indicators,” Proteomics, vol. 7, no. 24, pp. 4445–4456, 2007. View at Publisher · View at Google Scholar · View at Scopus
  105. A. Jungbauer and R. Hahn, “Ion-exchange chromatography,” Methods in Enzymology, vol. 463, pp. 349–371, 2009. View at Publisher · View at Google Scholar · View at Scopus
  106. B. D. Kelley, M. Switzer, P. Bastek et al., “High-throughput screening of chromatographic separations: IV. Ion-exchange,” Biotechnology and Bioengineering, vol. 100, no. 5, pp. 950–963, 2008. View at Publisher · View at Google Scholar
  107. K. S. Boos and C. H. Grimm, “High-performance liquid chromatography integrated solid-phase extraction in bioanalysis using restricted access precolumn packings,” Trends in Analytical Chemistry, vol. 18, no. 3, pp. 175–180, 1999. View at Publisher · View at Google Scholar · View at Scopus
  108. E. Machtejevras, G. Marko-Varga, C. Lindberg, D. Lubda, R. Hendriks, and K. K. Unger, “Profiling of endogenous peptides by multidimensional liquid chromatography: on-line automated sample cleanup for biomarker discovery in human urine,” Journal of Separation Science, vol. 32, no. 13, pp. 2223–2232, 2009. View at Publisher · View at Google Scholar · View at Scopus
  109. O. Willemsen, E. Machtejevas, and K. K. Unger, “Enrichment of proteinaceous materials on a strong cation-exchange diol silica restricted access material: protein-protein displacement and interaction effects,” Journal of Chromatography A, vol. 1025, no. 2, pp. 209–216, 2004. View at Publisher · View at Google Scholar · View at Scopus
  110. K. Račaityte, E. S.M. Lutz, K. K. Unger, D. Lubda, and K. S. Boos, “Analysis of neuropeptide Y and its metabolites by high-performance liquid chromatography-electrospray ionization mass spectrometry and integrated sample clean-up with a novel restricted-access sulphonic acid cation exchanger,” Journal of Chromatography A, vol. 890, no. 1, pp. 135–144, 2000. View at Publisher · View at Google Scholar
  111. K. Wagner, T. Miliotis, G. Marko-Varga, R. Bischoff, and K. K. Unger, “An automated on-line multidimensional HPLC system for protein and peptide mapping with integrated sample preparation,” Analytical Chemistry, vol. 74, no. 4, pp. 809–820, 2002. View at Publisher · View at Google Scholar · View at Scopus
  112. L. Hu, K. S. Boos, M. Ye, R. Wu, and H. Zou, “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,” Journal of Chromatography A, vol. 1216, no. 28, pp. 5377–5384, 2009. View at Publisher · View at Google Scholar · View at Scopus
  113. L. Rieux, R. Bischoff, E. Verpoorte, and H. A. G. Niederländer, “Restricted-access material-based high-molecular-weight protein depletion coupled on-line with nano-liquid chromatography-mass spectrometry for proteomics applications,” Journal of Chromatography A, vol. 1149, no. 2, pp. 169–177, 2007. View at Publisher · View at Google Scholar · View at Scopus
  114. S. Souverain, S. Rudaz, and J. L. Veuthey, “Restricted access materials and large particle supports for on-line sample preparation: an attractive approach for biological fluids analysis,” Journal of Chromatography B, vol. 801, no. 2, pp. 141–156, 2004. View at Publisher · View at Google Scholar
  115. K. Sandra, M. Moshir, F. D'hondt et al., “Highly efficient peptide separations in proteomics. Part 2: Bi- and multidimensional liquid-based separation techniques,” Journal of Chromatography B, vol. 877, no. 11-12, pp. 1019–1039, 2009. View at Publisher · View at Google Scholar
  116. J. Tang, M. Gao, C. Deng, and X. Zhang, “Recent development of multi-dimensional chromatography strategies in proteome research,” Journal of Chromatography B, vol. 866, no. 1-2, pp. 123–132, 2008. View at Publisher · View at Google Scholar
  117. I. François, K. Sandra, and P. Sandra, “Comprehensive liquid chromatography: fundamental aspects and practical considerations—a review,” Analytica Chimica Acta, vol. 641, no. 1-2, pp. 14–31, 2009. View at Publisher · View at Google Scholar · View at Scopus
  118. R. Aebersold and M. Mann, “Mass spectrometry-based proteomics,” Nature, vol. 422, no. 6928, pp. 198–207, 2003. View at Publisher · View at Google Scholar · View at Scopus
  119. X. Yuan and D. M. Desiderio, “Human cerebrospinal fluid peptidomics,” Journal of Mass Spectrometry, vol. 40, no. 2, pp. 176–181, 2005. View at Publisher · View at Google Scholar · View at Scopus
  120. J. A. Dowell, W. V. Heyden, and L. Li, “Rat neuropeptidomics by LC-MS/MS and MALDI-FTMS: enhanced dissection and extraction techniques coupled with 2D RP-RP HPLC,” Journal of Proteome Research, vol. 5, no. 12, pp. 3368–3375, 2006. View at Publisher · View at Google Scholar · View at Scopus