Proteomic challenges: Sample preparation techniques for Microgram-Quantity protein analysis from biological samples

International Journal of Molecular Sciences

Volumn 16, Issue 2, 2015, Pages 3537-3563

  Feist, Peter ^a   Hummon, Amanda B ^a  

^a UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

Mass limited samples; Mass spectrometry; Microgram samples; Proteins

Indexed keywords

MACROGOL; POLYETHYLENEIMINE; PROTEOME;

CAPILLARY ZONE ELECTROPHORESIS; CRITICAL MICELLE CONCENTRATION; ELECTROSPRAY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HYDROPHILIC INTERACTION CHROMATOGRAPHY; ISOELECTRIC POINT; LIQUID CHROMATOGRAPHY; MACROSCALE; MASS SPECTROMETRY; MEASUREMENT; PRECIPITATION; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEOMICS; REVIEW; ROBOTICS; SYSTEMATIC REVIEW; TUMOR BIOPSY; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; ULTRAFILTRATION; ANALYSIS; ANIMAL; MICROTECHNOLOGY; PROCEDURES;

MAMMALIA;

ANALYTIC SAMPLE PREPARATION METHODS; ANIMALS; HUMANS; MASS SPECTROMETRY; MICROTECHNOLOGY; PROTEOME; PROTEOMICS;

EID: 84922386015     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms16023537     Document Type: Review

References (167)

1. Wilson, R. Sensitivity and specificity: Twin goals of proteomics assays. Can they be combined? Expert Rev. Proteomics 2013, 10, 135-149.
2. Tonge, R.; Shaw, J.; Middleton, B.; Rowlinson, R.; Rayner, S.; Young, J.; Pognan, F.; Hawkins, E.; Currie, I.; Davison, M. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 2001, 1, 377-396.
3. Lilley, K.S.; Friedman, D.B. All about DIGE: Quantification technology for differential-display 2D-gel proteomics. Expert Rev. Proteomics 2004, 1, 401-409.
4. Karas, M.; Hillenkamp, F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 1988, 60, 2299-2301.
5. Tanaka, K.; Waki, H.; Ido, Y.; Akita, S.; Yoshida, Y.; Yoshida, T.; Matsuo, T. Protein and polymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 1988, 2, 151-153.
6. Fenn, J.B.; Mann, M.; Meng, C.K.; Wong, S.F.; Whitehouse, C.M. Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246, 64-71.
7. Weaver, E.M.; Hummon, A.B. Imaging mass spectrometry: From tissue sections to cell cultures. Adv. Drug Deliv. Rev. 2013, 65, 1039-1055.
8. Gutstein, H.B.; Morris, J.S.; Annangudi, S.P.; Sweedler, J.V. Microproteomics: Analysis of protein diversity in small samples. Mass Spectrom. Rev. 2008, 27, 316-330.
9. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
10. Scigelova, M.; Makarov, A. Orbitrap mass analyzer—Overview and applications in proteomics. Proteomics 2006, 6, 16-21.
11. Ahlf, D.R.; Compton, P.D.; Tran, J.C.; Early, B.P.; Thomas, P.M.; Kelleher, N.L. Evaluation of the compact high-field orbitrap for top-down proteomics of human cells. J. Proteome Res. 2012, 11, 4308-4314.
12. Hebert, A.S.; Richards, A.L.; Bailey, D.J.; Ulbrich, A.; Coughlin, E.E.; Westphall, M.S.; Coon, J.J. The one hour yeast proteome. Mol. Cell. Proteomics 2014, 13, 339-347.
13. Mann, M.; Kelleher, N.L. Precision proteomics: The case for high resolution and high mass accuracy. Proc. Natl. Acad. Sci. USA 2008, 105, 18132-18138.
14. Stahl-Zeng, J.; Lange, V.; Ossola, R.; Eckhardt, K.; Krek, W.; Aebersold, R.; Domon, B. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 2007, 6, 1809-1817.
15. Lin, S.; Shaler, T.A.; Becker, C.H. Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap. Anal. Chem. 2006, 78, 5762-5767.
16. March, R.E.; Todd, J.F.J. Practical Aspects of Trapped Ion Mass Spectrometry, Volume 4: Theory and Instrumentation; CRC Press: Boca Raton, FL, USA, 2010; pp. 61-64.
17. Dancík, V.; Addona, T.A.; Clauser, K.R.; Vath, J.E.; Pevzner, P.A. De novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. 1999, 6, 327-342.
18. Medzihradszky, K.F.; Chalkley, R.J. Lessons in de novo peptide sequencing by tandem mass spectrometry. Mass Spectrom. Rev. 2015, 34, 43-63.
19. Thiede, B.; Höhenwarter, W.; Krah, A.; Mattow, J.; Schmid, M.; Schmidt, F.; Jungblut, P.R. Peptide mass fingerprinting. Methods (San Diego Calif.) 2005, 35, 237-247.
20. Webster, J.; Oxley, D. Peptide mass fingerprinting: Protein identification using MALDI-TOF mass spectrometry. Methods Mol. Biol. (Clifton N.J.) 2005, 310, 227-240.
21. Pappin, D.J.; Hojrup, P.; Bleasby, A.J. Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 1993, 3, 327-332.
22. Sommerer, N.; Centeno, D.; Rossignol, M. Peptide mass fingerprinting. In Plant Proteomics; Thiellement, H., Zivy, M., Damerval, C., Méchin, V., Eds.; Humana Press: New York, NY, USA, 2007; pp. 219-234.
23. Mao, Y.; Valeja, S.G.; Rouse, J.C.; Hendrickson, C.L.; Marshall, A.G. Top-down structural analysis of an intact monoclonal antibody by electron capture dissociation-Fourier transform ion cyclotron resonance-mass spectrometry. Anal. Chem. 2013, 85, 4239-4246.
24. Syka, J.E.P.; Coon, J.J.; Schroeder, M.J.; Shabanowitz, J.; Hunt, D.F. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA 2004, 101, 9528-9533.
25. Zhurov, K.O.; Fornelli, L.; Wodrich, M.D.; Laskay, Ü.A.; Tsybin, Y.O. Principles of electron capture and transfer dissociation mass spectrometry applied to peptide and protein structure analysis. Chem. Soc. Rev. 2013, 42, 5014-5030.
26. Jedrychowski, M.P.; Huttlin, E.L.; Haas, W.; Sowa, M.E.; Rad, R.; Gygi, S.P. Evaluation of HCD and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Mol. Cell. Proteomics 2011, 10, doi:10.1074/mcp.M111.009910.
27. Michalski, A.; Neuhauser, N.; Cox, J.; Mann, M. A systematic investigation into the nature of tryptic HCD spectra. J. Proteome Res. 2012, 11, 5479-5491.
28. Papayannopoulos, I.A. The interpretation of collision-induced dissociation tandem mass spectra of peptides. Mass Spectrom. Rev. 1995, 14, 49-73.
29. Medzihradszky, K.F.; Campbell, J.M.; Baldwin, M.A.; Falick, A.M.; Juhasz, P.; Vestal, M.L.; Burlingame, A.L. The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal. Chem. 2000, 72, 552-558.
30. O’Brien, J.P.; Brodbelt, J.S. Structural characterization of gangliosides and glycolipids via ultraviolet photodissociation mass spectrometry. Anal. Chem. 2013, 85, 10399-10407.
31. Brodbelt, J.S. Photodissociation mass spectrometry: New tools for characterization of biological molecules. Chem. Soc. Rev. 2014, 43, 2757-2783.
32. Keough, T.; Youngquist, R.S.; Lacey, M.P. A method for high-sensitivity peptide sequencing using postsource decay matrix-assisted laser desorption ionization mass spectrometry. Proc. Natl. Acad. Sci. USA 1999, 96, 7131-7136.
33. Shen, Y.; Tolić, N.; Xie, F.; Zhao, R.; Purvine, S.O.; Schepmoes, A.A.; Moore, R.J.; Anderson, G.A.; Smith, R.D. Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: Comparison of peptide identification methods. J. Proteome Res. 2011, 10, 3929-3943.
34. Scott, C.T.; Caulfield, T.; Borgelt, E.; Illes, J. Personal medicine The new banking crisis. Nat. Biotechnol. 2012, 30, 141-147.
35. Guidelines for the Use of Human Tissue for Future Unspecified Research Purposes. Available online: http://www.health.govt.nz/publication/guidelines-use-human-tissue-future-unspecified-research-purposes-0(accessed on 31 October 2014).
36. Salvaterra, E.; Lecchi, L.; Giovanelli, S.; Butti, B.; Bardella, M.T.; Bertazzi, P.A.; Bosari, S.; Coggi, G.; Coviello, D.A.; Lalatta, F., et al. Banking together. A unified model of informed consent for biobanking. EMBO Rep. 2008, 9, 307-313.
37. Raynie, D.E. Modern extraction techniques. Anal. Chem. 2010, 82, 4911-4916.
38. Cañas, B.; Piñeiro, C.; Calvo, E.; López-Ferrer, D.; Gallardo, J.M. Trends in sample preparation for classical and second generation proteomics. J. Chromatogr. 2007, 1153, 235-258.
39. Traditional Methods of Cell Lysis. Available online: http://www.piercenet.com/method/traditional-methods-cell-lysis(accessed on 31 October 2014).
40. Detergents for Cell Lysis and Protein Extraction. Available online: http://www.piercenet.com/method/detergents-cell-lysis-protein-extraction(accessed on 31 October 2014).
41. Swiderek, K.M.; Alpert, A.J.; Heckendorf, A.; Nugent, K.; Patterson, S.D. Structural analysis of proteins and peptides in the presence of detergents: Tricks of the trade. ABRF News Artic. Methodol. 1997, 8, 17-25.
42. Bodzon-Kulakowska, A.; Bierczynska-Krzysik, A.; Dylag, T.; Drabik, A.; Suder, P.; Noga, M.; Jarzebinska, J.; Silberring, J. Methods for samples preparation in proteomic research. J. Chromatogr. 2007, 849, 1-31.
43. Visser, N.F.C.; Lingeman, H.; Irth, H. Sample preparation for peptides and proteins in biological matrices prior to liquid chromatography and capillary zone electrophoresis. Anal. Bioanal. Chem. 2005, 382, 535-558.
44. Hilbrig, F.; Freitag, R. Protein purification by affinity precipitation. J. Chromatogr. 2003, 790, 79-90.
45. Zhou, J.-Y.; Dann, G.P.; Shi, T.; Wang, L.; Gao, X.; Su, D.; Nicora, C.D.; Shukla, A.K.; Moore, R.J.; Liu, T., et al. Simple sodium dodecyl sulfate-assisted sample preparation method for LC-MS-based proteomics applications. Anal. Chem. 2012, 84, 2862-2867.
46. Buxton, T.B.; Crockett, J.K.; Moore, W.L.; Moore, W.L.; Rissing, J.P. Protein precipitation by acetone for the analysis of polyethylene glycol in intestinal perfusion fluid. Gastroenterology 1979, 76, 820-824.
47. Peterson, G.L. A simplification of the protein assay method of Lowry et al. which is more generally applicable. Anal. Biochem. 1977, 83, 346-356.
48. Bensadoun, A.; Weinstein, D. Assay of proteins in the presence of interfering materials. Anal. Biochem. 1976, 70, 241-250.
49. Arnold, U.; Ulbrich-Hofmann, R. Quantitative protein precipitation from guanidine hydrochloride-containing solutions by sodium deoxycholate/trichloroacetic acid. Anal. Biochem. 1999, 271, 197-199.
50. Wessel, D.; Flügge, U.-I. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 1984, 138, 141-143.
51. Yeung, Y.-G.; Stanley, E.R. Rapid detergent removal from peptide samples with ethyl acetate for mass spectrometry analysis. Curr. Protoc. Protein Sci. 2010, doi:10.1002/0471140864.ps1612s59.
52. Yeung, Y.-G.; Nieves, E.; Angeletti, R.H.; Stanley, E.R. Removal of detergents from protein digests for mass spectrometry analysis. Anal. Biochem. 2008, 382, 135-137.
53. Levin, B.; Oberholzer, V.G.; Whitehead, T.P. Serum protein fractions: A comparison of precipitation methods with electrophoresis. J. Clin. Pathol. 1950, 3, 260.
54. Fic, E.; Kedracka-Krok, S.; Jankowska, U.; Pirog, A.; Dziedzicka-Wasylewska, M. Comparison of protein precipitation methods for various rat brain structures prior to proteomic analysis. Electrophoresis 2010, 31, 3573-3579.
55. Rabilloud, T. Detergents and chaotropes for protein solubilization before two-dimensional electrophoresis. Methods Mol. Biol. (Clifton N.J.) 2009, 528, 259-267.
56. Chapel, A.; Salvi, D.; Garin, J.; Joyard, J.; de Biologie, D.; et Structurale, M.; VØgØtale, C.; Fourier, U.J. Organic solvent extraction as a versatile procedure to identify hydrophobic chloroplast membrane proteins. Electrophoresis 2000, 21, 3517-3526.
57. Englard, S.; Seifter, S. Precipitation techniques. Methods Enzymol. 1990, 182, 285-300.
58. Burgess, R.R. Protein precipitation techniques. Methods Enzymol. 2009, 463, 331-342.
59. Jiang, L.; He, L.; Fountoulakis, M. Comparison of protein precipitation methods for sample preparation prior to proteomic analysis. J. Chromatogr. 2004, 1023, 317-320.
60. Wiśniewski, J.R.; Zielinska, D.F.; Mann, M. Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method. Anal. Biochem. 2011, 410, 307-309.
61. Gupta, M.N.; Kaul, R.; Guoqiang, D.; Dissing, U.; Mattiasson, B. Affinity precipitation of proteins. J. Mol. Recognit. 1996, 9, 356-359.
62. Holler, C.; Vaughan, D.; Zhang, C. Polyethyleneimine precipitation versus anion exchange chromatography in fractionating recombinant β-glucuronidase from transgenic tobacco extract. J. Chromatogr. 2007, 1142, 98-105.
63. Hegg, P.O. Precipitation of egg white proteins below their isoelectric points by sodium dodecyl sulphate and temperature. Biochim. Biophys. Acta 1979, 579, 73-87.
64. Jaffé, W.G. A simple method for the approximate estimation of the isoelectric point of soluble proteins. J. Biol. Chem. 1943, 148, 185-186.
65. Fan, J.; Huang, B.; Wang, X.; Zhang, X.C. Thermal precipitation fluorescence assay for protein stability screening. J. Struct. Biol. 2011, 175, 465-468.
66. Hill, A.R.; Irvine, D.M. Effects of pH on the thermal precipitation of proteins in acid and sweet cheese wheys. Can. Inst. Food Sci. Technol. J. 1988, 21, 386-389.
67. Ingham, K.C. Precipitation of proteins with polyethylene glycol. Methods Enzymol. 1990, 182, 301-306.
68. Ingham, K.C. Protein precipitation with polyethylene glycol. Methods Enzymol. 1984, 104, 351-356.
69. Sim, S.-L.; He, T.; Tscheliessnig, A.; Mueller, M.; Tan, R.B.H.; Jungbauer, A. Protein precipitation by polyethylene glycol: A generalized model based on hydrodynamic radius. J. Biotechnol. 2012, 157, 315-319.
70. Crowell, A.M.J.; Wall, M.J.; Doucette, A.A. Maximizing recovery of water-soluble proteins through acetone precipitation. Anal. Chim. Acta 2013, 796, 48-54.
71. Barritault, D.; Expert-Bezançon, A.; Guérin, M.-F.; Hayes, D. The use of acetone precipitation in the isolation of ribosomal proteins. Eur. J. Biochem. 1976, 63, 131-135.
72. Puchades, M.; Westman, A.; Blennow, K.; Davidsson, P. Analysis of intact proteins from cerebrospinal fluid by matrix-assisted laser desorption/ionization mass spectrometry after two-dimensional liquid-phase electrophoresis. Rapid Commun. Mass Spectrom. 1999, 13, 2450-2455.
73. Thongboonkerd, V.; Mcleish, K.R.; Arthur, J.M.; Klein, J.B. Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int. 2002, 62, 1461-1469.
74. Srivastava, O.P.; Srivastava, K. Purification of gamma-crystallin from human lenses by acetone precipitation method. Curr. Eye Res. 1998, 17, 1074-1081.
75. Von Hagen, J. Proteomics Sample Preparation; John Wiley & Sons Inc.: Hoboken, NJ, USA, 2011.
76. Wu, X.; Xiong, E.; Wang, W.; Scali, M.; Cresti, M. Universal sample preparation method integrating trichloroacetic acid/acetone precipitation with phenol extraction for crop proteomic analysis. Nat. Protoc. 2014, 9, 362-374.
77. Chevallet, M.; Diemer, H.; van Dorssealer, A.; Villiers, C.; Rabilloud, T. Toward a better analysis of secreted proteins: The example of the myeloid cells secretome. Proteomics 2007, 7, 1757-1770.
78. Robinson, P.J.; Liu, J.P.; Chen, W.; Wenzel, T. Activation of protein kinase C in vitro and in intact cells or synaptosomes determined by acetic acid extraction of MARCKS. Anal. Biochem. 1993, 210, 172-178.
79. Isaacson, T.; Damasceno, C.M.B.; Saravanan, R.S.; He, Y.; Catalá, C.; Saladié, M.; Rose, J.K.C. Sample extraction techniques for enhanced proteomic analysis of plant tissues. Nat. Protoc. 2006, 1, 769-774.
80. Duan, X.; Young, R.; Straubinger, R.M.; Page, B.; Cao, J.; Wang, H.; Yu, H.; Canty, J.M.; Qu, J. A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteome. J. Proteome Res. 2009, 8, 2838-2850.
81. De Godoy, L.M.F.; Olsen, J.V.; Cox, J.; Nielsen, M.L.; Hubner, N.C.; Fröhlich, F.; Walther, T.C.; Mann, M. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455, 1251-1254.
82. Li, N.; Shaw, A.R.E.; Zhang, N.; Mak, A.; Li, L. Lipid raft proteomics: Analysis of in-solution digest of sodium dodecyl sulfate-solubilized lipid raft proteins by liquid chromatography-matrix-assisted laser desorption/ionization tandem mass spectrometry. Proteomics 2004, 4, 3156-3166.
83. De Souza, G.A.; Godoy, L.M.F.; Mann, M. Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors. Genome Biol. 2006, 7, R72.
84. Go, E.P.; Rebecchi, K.R.; Desaire, H. In-solution digestion of glycoproteins for glycopeptide-based mass analysis. Methods Mol. Biol. (Clifton N.J.) 2013, 951, 103-111.
85. Lasonder, E.; Ishihama, Y.; Andersen, J.S.; Vermunt, A.M.W.; Pain, A.; Sauerwein, R.W.; Eling, W.M.C.; Hall, N.; Waters, A.P.; Stunnenberg, H.G., et al. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 2002, 419, 537-542.
86. Pomastowski, P.; Buszewski, B. Two-dimensional gel electrophoresis in the light of new developments. TrAC Trends Anal. Chem. 2014, 53, 167-177.
87. Shevchenko, A.; Wilm, M.; Vorm, O.; Mann, M. Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal. Chem. 1996, 68, 850-858.
88. Herbert, B. Advances in protein solubilisation for two-dimensional electrophoresis. Electrophoresis 1999, 20, 660-663.
89. Görg, A.; Weiss, W.; Dunn, M.J. Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004, 4, 3665-3685.
90. Rabilloud, T. Two-dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains. Proteomics 2002, 2, 3-10.
91. Rabilloud, T.; Chevallet, M.; Luche, S.; Lelong, C. Two-dimensional gel electrophoresis in proteomics: Past, present and future. J. Proteomics 2010, 73, 2064-2077.
92. Granvogl, B.; Plöscher, M.; Eichacker, L.A. Sample preparation by in-gel digestion for mass spectrometry-based proteomics. Anal. Bioanal. Chem. 2007, 389, 991-1002.
93. Shevchenko, A.; Tomas, H.; Havlis, J.; Olsen, J.V.; Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 2006, 1, 2856-2860.
94. Thakur, D.; Rejtar, T.; Wang, D.; Bones, J.; Cha, S.; Clodfelder-Miller, B.; Richardson, E.; Binns, S.; Dahiya, S.; Sgroi, D., et al. Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry. J. Chromatogr. 2011, 1218, 8168-8174.
95. Rabilloud, T.; Lelong, C. Two-dimensional gel electrophoresis in proteomics: A tutorial. J. Proteomics 2011, 74, 1829-1841.
96. Craven, R.A.; Totty, N.; Harnden, P.; Selby, P.J.; Banks, R.E. Laser capture microdissection and two-dimensional polyacrylamide gel electrophoresis. Am. J. Pathol. 2002, 160, 815-822.
97. Weiner, A.M.; Platt, T.; Weber, K. Amino-terminal sequence analysis of proteins purified on a nanomole scale by gel electrophoresis. J. Biol. Chem. 1972, 247, 3242-3251.
98. Speicher, K.; Kolbas, O.; Harper, S.; Speicher, D. Systematic analysis of peptide recoveries from in-gel digestions for protein identifications in proteome studies. J. Biomol. Tech. 2000, 11, 74-86.
99. Gundry, R.L.; White, M.Y.; Murray, C.I.; Kane, L.A.; Fu, Q.; Stanley, B.A.; van Eyk, J.E. Preparation of proteins and peptides for mass spectrometry analysis in a bottom-up proteomics workflow. Curr. Protoc. Mol. Biol. 2009, doi:10.1002/0471142727.mb1025s88.
100. Zhou, S.; Bailey, M.J.; Dunn, M.J.; Preedy, V.R.; Emery, P.W. A quantitative investigation into the losses of proteins at different stages of a two-dimensional gel electrophoresis procedure. Proteomics 2005, 5, 2739-2747.
101. Manza, L.L.; Stamer, S.L.; Ham, A.-J.L.; Codreanu, S.G.; Liebler, D.C. Sample preparation and digestion for proteomic analyses using spin filters. Proteomics 2005, 5, 1742-1745.
102. Wang, X. Bioinformatics of Human Proteomics; Springer Science + Business Media B.V.: Dordrecht, The Netherlands, 2013.
103. Wiśniewski, J.R.; Zougman, A.; Nagaraj, N.; Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 2009, 6, 359-362.
104. Erde, J.; Loo, R.R.O.; Loo, J.A. Enhanced FASP (eFASP) to increase proteome coverage and sample recovery for quantitative proteomic experiments. J. Proteome Res. 2014, 13, 1885-1895.
105. Zielinska, D.F.; Gnad, F.; Wiśniewski, J.R.; Mann, M. Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell 2010, 141, 897-907.
106. Kanshin, E.; Michnick, S.; Thibault, P. Sample preparation and analytical strategies for large-scale phosphoproteomics experiments. Semin. Cell Dev. Biol. 2012, 23, 843-853.
107. Wiśniewski, J.R.; Mann, M. Reply to “Spin filter-based sample preparation for shotgun proteomics”. Nat. Methods 2009, 6, 785-786.
108. Eggler, A.L.; Luo, Y.; van Breemen, R.B.; Mesecar, A.D. Identification of the highly reactive cysteine 151 in the chemopreventive agent-sensor Keap1 protein is method-dependent. Chem. Res. Toxicol. 2007, 20, 1878-1884.
109. Liebler, D.C.; Ham, A.-J.L. Spin filter-based sample preparation for shotgun proteomics. Nat. Methods 2009, 6, 785.
110. Wiśniewski, J.R.; Ostasiewicz, P.; Mann, M. High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J. Proteome Res. 2011, 10, 3040-3049.
111. Weston, L.A.; Bauer, K.M.; Hummon, A.B. Comparison of bottom-up proteomic approaches for LC-MS analysis of complex proteomes. Anal. Methods 2013, 5, 4615-4621.
112. Washburn, M.P.; Wolters, D.; Yates, J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19, 242-247.
113. Lipton, M.S.; Pasa-Tolic, L.; Anderson, G.A.; Anderson, D.J.; Auberry, D.L.; Battista, J.R.; Daly, M.J.; Fredrickson, J.; Hixson, K.K.; Kostandarithes, H., et al. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc. Natl. Acad. Sci. USA 2002, 99, 11049-11054.
114. Xie, F.; Liu, T.; Qian, W.-J.; Petyuk, V.A.; Smith, R.D. Liquid chromatography-mass spectrometry-based quantitative proteomics. J. Biol. Chem. 2011, 286, 25443-25449.
115. Peng, J.; Elias, J.E.; Thoreen, C.C.; Licklider, L.J.; Gygi, S.P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J. Proteome Res. 2003, 2, 43-50.
116. Jungblut, P.R. Protein and Peptide Mass Spectrometry in Drug Discovery; Gross, M.L., Chen, G., Pramanik, B., Eds.; ChemMedChem: Weinheim, Germany, 2012; Volume 7, pp. 2241-2242.
117. You, J.; Wang, L.; Saji, M.; Olesik, S.V.; Ringel, M.D.; Lucas, D.M.; Byrd, J.C.; Freitas, M.A. High-sensitivity TFA-free LC-MS for profiling histones. Proteomics 2011, 11, 3326-3334.
118. Li, H.; James, C.A. LC-MS bioanalysis of peptides and polypeptides. In Handbook of LC-MS Bioanalysis; Li, W., Zhang, J., Tse, F.L.S., Eds.; John Wiley & Sons Inc.: Hoboken, NJ, USA, 2013; pp. 535-549.
119. De Jong, E.P.; Griffin, T.J. Online nanoscale ERLIC-MS outperforms RPLC-MS for shotgun proteomics in complex mixtures. J. Proteome Res. 2012, 11, 5059-5064.
120. Hao, P.; Qian, J.; Dutta, B.; Cheow, E.S.H.; Sim, K.H.; Meng, W.; Adav, S.S.; Alpert, A.; Sze, S.K. Enhanced separation and characterization of deamidated peptides with RP-ERLIC-based multidimensional chromatography coupled with tandem mass spectrometry. J. Proteome Res. 2012, 11, 1804-1811.
121. Zarei, M.; Sprenger, A.; Metzger, F.; Gretzmeier, C.; Dengjel, J. Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches. J. Proteome Res. 2011, 10, 3474-3483.
122. Hao, P.; Guo, T.; Li, X.; Adav, S.S.; Yang, J.; Wei, M.; Sze, S.K. Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: Comprehensive profiling of rat kidney proteome. J. Proteome Res. 2010, 9, 3520-3526.
123. Wang, H.; Qian, W.-J.; Mottaz, H.M.; Clauss, T.R.W.; Anderson, D.J.; Moore, R.J.; Camp, D.G.; Khan, A.H.; Sforza, D.M.; Pallavicini, M., et al. Development and evaluation of a micro and nanoscale proteomic sample preparation method. J. Proteome Res. 2005, 4, 2397-2403.
124. Emmert-Buck, M.R.; Gillespie, J.W.; Paweletz, C.P.; Ornstein, D.K.; Basrur, V.; Appella, E.; Wang, Q.H.; Huang, J.; Hu, N.; Taylor, P., et al. An approach to proteomic analysis of human tumors. Mol. Carcinog. 2000, 27, 158-165.
125. Gozal, Y.M.; Cheng, D.; Duong, D.M.; Lah, J.J.; Levey, A.I.; Peng, J. Merger of laser capture microdissection and mass spectrometry: A window into the amyloid plaque proteome. Methods Enzymol. 2006, 412, 77-93.
126. Picotti, P.; Bodenmiller, B.; Mueller, L.N.; Domon, B.; Aebersold, R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 2009, 138, 795-806.
127. Anderson, N.L.; Anderson, N.G. The human plasma proteome: History, character, and diagnostic prospects. Mol. Cell. Proteomics 2002, 1, 845-867.
128. Mitchell, P. Proteomics retrenches. Nat. Biotechnol. 2010, 28, 665-670.
129. Wang, N.; Xu, M.; Wang, P.; Li, L. Development of mass spectrometry-based shotgun method for proteome analysis of 500 to 5000 cancer cells. Anal. Chem. 2010, 82, 2262-2271.
130. Sun, L.; Bertke, M.M.; Champion, M.M.; Zhu, G.; Huber, P.W.; Dovichi, N.J. Quantitative proteomics of Xenopus laevis embryos: Expression kinetics of nearly 4000 proteins during early development. Sci. Rep. 2014, 4, 4365.
131. Sleno, L. The use of mass defect in modern mass spectrometry. JMS 2012, 47, 226-236.
132. Sun, L.; Zhu, G.; Dovichi, N.J. Comparison of the LTQ-Orbitrap Velos and the Q-Exactive for proteomic analysis of 1-1000 ng RAW 264.7 cell lysate digests. Rapid Commun. Mass Spectrom. 2013, 27, 157-162.
133. Meyer, J.G.; Komives, E.A. Charge state coalescence during electrospray ionization improves peptide identification by tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 2012, 23, 1390-1399.
134. Hahne, H.; Pachl, F.; Ruprecht, B.; Maier, S.K.; Klaeger, S.; Helm, D.; Médard, G.; Wilm, M.; Lemeer, S.; Kuster, B. DMSO enhances electrospray response, boosting sensitivity of proteomic experiments. Nat. Methods 2013, 10, 989-991.
135. Tjernberg, A.; Markova, N.; Griffiths, W.J.; Hallén, D. DMSO-related effects in protein characterization. J. Biomol. Screen. 2006, 11, 131-137.
136. Korfmacher, W.A. Using Mass Spectrometry for Drug Metabolism Studies, 2nd ed.; CRC Press: Boca Raton, FL, USA, 2009.
137. Brash, J.L.; ten Hove, P. Effect of plasma dilution on adsorption of fibrinogen to solid surfaces. Thromb. Haemost. 1984, 51, 326-330.
138. Horbett, T.A. Chapter 13 Principles underlying the role of adsorbed plasma proteins in blood interactions with foreign materials. Cardiovasc. Pathol. 1993, 2, 137-148.
139. Hervey, W.J.; Strader, M.B.; Hurst, G.B. Comparison of digestion protocols for microgram quantities of enriched protein samples. J. Proteome Res. 2007, 6, 3054-3061.
140. Strader, M.B.; Tabb, D.L.; Hervey, W.J.; Pan, C.; Hurst, G.B. Efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems. Anal. Chem. 2006, 78, 125-134.
141. Kim, S.C.; Chen, Y.; Mirza, S.; Xu, Y.; Lee, J.; Liu, P.; Zhao, Y. A clean, more efficient method for in-solution digestion of protein mixtures without detergent or urea. J. Proteome Res. 2006, 5, 3446-3452.
142. Walsh, G. Proteins: Biochemistry and Biotechnology; John Wiley & Sons Inc.: Hoboken, NJ, USA, 2002.
143. Puchades, M.; Westman, A.; Blennow, K.; Davidsson, P. Removal of sodium dodecyl sulfate from protein samples prior to matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 1999, 13, 344-349.
144. Stone, K.L.; Williams, K.R. 2-Enzymatic digestion of proteins and HPLC peptide isolation. In A Practical Guide to Protein and Peptide Purification for Microsequencing, 2nd ed.; Matsudaira, P., Ed.; Academic Press: San Diego, CA, USA, 1993; pp. 43-69.
145. Walker, J.M. The Proteomics Protocols Handbook; Humana Press: New York, NY, USA, 2005.
146. Zhou, J.; Zhou, T.; Cao, R.; Liu, Z.; Shen, J.; Chen, P.; Wang, X.; Liang, S. Evaluation of the application of sodium deoxycholate to proteomic analysis of rat hippocampal plasma membrane. J. Proteome Res. 2006, 5, 2547-2553.
147. McDowell, G.S.; Gaun, A.; Steen, H. iFASP: Combining isobaric mass tagging with filter-aided sample preparation. J. Proteome Res. 2013, 12, 3809-3812.
148. Huber, M.L.; Sacco, R.; Parapatics, K.; Skucha, A.; Khamina, K.; Muller, A.C.; Rudashevskaya, E.L.; Bennett, K.L. abFASP-MS: Affinity-based filter-aided sample preparation mass spectrometry for quantitative analysis of chemically labeled protein complexes. J. Proteome Res. 2014, 13, 1147-1155.
149. Cha, S.; Imielinski, M.B.; Rejtar, T.; Richardson, E.A.; Thakur, D.; Sgroi, D.C.; Karger, B.L. In Situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection: Annotation by protein set enrichment analysis and gene ontology. Mol. Cell. Proteomics 2010, 9, 2529-2544.
150. Jorgenson, J.W.; Lukacs, K.D. Zone electrophoresis in open-tubular glass capillaries. Anal. Chem. 1981, 53, 1298-1302.
151. Karger, B.L.; Guttman, A. DNA sequencing by capillary electrophoresis. Electrophoresis 2009, 30, S196-S202.
152. Heemskerk, A.A.M.; Deelder, A.M.; Mayboroda, O.A. CE-ESI-MS for bottom-up proteomics: Advances in separation, interfacing and applications. Mass Spectrom. Rev. 2014, doi:10.1002/mas.21432.
153. Li, Y.; Champion, M.M.; Sun, L.; Champion, P.A.D.; Wojcik, R.; Dovichi, N.J. Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry as an alternative proteomics platform to ultraperformance liquid chromatography-electrospray ionization-tandem mass spectrometry for samples of intermediate complexity. Anal. Chem. 2012, 84, 1617-1622.
154. Sun, L.; Zhu, G.; Yan, X.; Champion, M.M.; Dovichi, N.J. Capillary zone electrophoresis for analysis of complex proteomes using an electrokinetically pumped sheath flow nanospray interface. Proteomics 2014, 14, 622-628.
155. Sun, L.; Zhu, G.; Mou, S.; Zhao, Y.; Champion, M.M.; Dovichi, N.J. Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for quantitative parallel reaction monitoring of peptide abundance and single-shot proteomic analysis of a human cell line. J. Chromatogr. 2014, 1359, 303-308.
156. Zhu, G.; Sun, L.; Yan, X.; Dovichi, N.J. Stable, reproducible, and automated capillary zone electrophoresis-tandem mass spectrometry system with an electrokinetically pumped sheath-flow nanospray interface. Anal. Chim. Acta 2014, 810, 94-98.
157. Zhu, G.; Sun, L.; Yan, X.; Dovichi, N.J. Single-shot proteomics using capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry with production of more than 1250 Escherichia coli peptide identifications in a 50 min separation. Anal. Chem. 2013, 85, 2569-2573.
158. Li, Y.; Compton, P.D.; Tran, J.C.; Ntai, I.; Kelleher, N.L. Optimizing capillary electrophoresis for top-down proteomics of 30-80 kDa proteins. Proteomics 2014, 14, 1158-1164.
159. Zhao, Y.; Sun, L.; Champion, M.M.; Knierman, M.D.; Dovichi, N.J. Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for top-down characterization of the Mycobacterium marinum secretome. Anal. Chem. 2014, 86, 4873-4878.
160. Diamond, D.L.; Jacobs, J.M.; Paeper, B.; Proll, S.C.; Gritsenko, M.A.; Carithers, R.L.; Larson, A.M.; Yeh, M.M.; Camp, D.G.; Smith, R.D., et al. Proteomic profiling of human liver biopsies: Hepatitis C virus-induced fibrosis and mitochondrial dysfunction. Hepatol. (Baltim. Md.) 2007, 46, 649-657.
161. Gerlinger, M.; Rowan, A.J.; Horswell, S.; Larkin, J.; Endesfelder, D.; Gronroos, E.; Martinez, P.; Matthews, N.; Stewart, A.; Tarpey, P., et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 2012, 366, 883-892.
162. Cancer Symptoms, Causes, Treatment—How is cancer diagnosed? Available online: http://www.medicinenet.com/cancer/article.htm(accessed on 3 November 2014).
163. Bruening, W.; Schoelles, K.; Treadwell, J.; Launders, J.; Fontanarosa, J.; Tipton, K. Comparative Effectiveness of Core-Needle and Open Surgical Biopsy for the Diagnosis of Breast Lesions; AHRQ Comparative Effectiveness Reviews; Agency for Healthcare Research and Quality (US): Rockville, MD, USA, 2009.
164. Breast Biopsy Cancer & Biopsies Susan G. Komen®. Available online: http://ww5.komen.org/BreastCancer/Biopsies.html (accessed on 3 November 2014).
165. Rodenburg, W.; Pennings, J.L.A.; van Oostrom, C.T.M.; Roodbergen, M.; Kuiper, R.V.; Luijten, M.; de Vries, A. Identification of breast cancer biomarkers in transgenic mouse models: A proteomics approach. Proteomics Clin. Appl. 2010, 4, 603-612.
166. Taguchi, A.; Politi, K.; Pitteri, S.J.; Lockwood, W.W.; Faça, V.M.; Kelly-Spratt, K.; Wong, C.-H.; Zhang, Q.; Chin, A.; Park, K.-S., et al. Lung cancer signatures in plasma based on proteome profiling of mouse tumor models. Cancer Cell 2011, 20, 289-299.
167. Feist, P; Sun, L; Liu, X; Dovichi, N.J.; Hummon, A.B. Bottom-up proteomic analysis of single HCT 116 colon carcinoma multicellular spheroids. Rapid Commun. Mass Spectrom. 2015, in press.