Power and limitations of electrophoretic separations in proteomics strategies

Mass Spectrometry Reviews

Volumn 28, Issue 5, 2009, Pages 816-843

  Rabilloud, Thierry ^a,b   Vaezzadeh, Ali R ^c   Potier, Noelle ^b   Lelong, Cécile ^a,d   Leize Wagner, Emmanuelle ^b   Chevallet, Mireille ^a,b  

^a CEA GRENOBLE   (France)

^b CNRS   (France)

^c GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^d UNIV GRENOBLE ALPES   (France)

Author keywords

Electrophoresis; Immobilized ph gradients; Isoelectric focusing; Peptides; Proteins; Proteomics; Two dimensional electrophoresis

Indexed keywords

CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PEPTIDES; PROTEINS; SEPARATION;

ELECTROPHORETIC SEPARATIONS; GEL ELECTROPHORESIS; ISOELECTRIC FOCUSING; LARGE-SCALE ANALYSIS; PH GRADIENTS; PROTEOMICS; SEPARATION TECHNIQUES; TWO DIMENSIONAL ELECTROPHORESIS;

ELECTROPHORESIS;

EID: 69849103563     PISSN: 02777037     EISSN: None     Source Type: Journal    
DOI: 10.1002/mas.20204     Document Type: Review

References (227)

1. Aebersold RH, Leavitt J, Saavedra RA, Hood LE, Kent SB. 1987. Internal amino acid sequence analysis of proteins separated by one-or twodimensional gel electrophoresis after in situ protease digestion on nitrocellulose. Proc Natl Acad Sci USA 84: 6970-6974.
2. An Y, Fu Z, Gutierrez P, Fenselau C. 2005. Solution isoelectric focusing for peptide analysis: Comparative investigation of an insoluble nuclear protein fraction. J Proteome Res 4: 2126-2132.
3. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI. 2002. Directed proteomic analysis of the human nucleolus. Curr Biol 12: 1-11.
4. Anderson L, Anderson NG. 1977. High resolution two-dimensional electrophoresis of human plasma proteins. Proc Natl Acad Sci USA 74: 5421-5425.
5. Anderson NG, Anderson NL. 1978a. Analytical techniques for cell fractions. XXI. Two-dimensional analysis of serum and tissue proteins: Multiple isoelectric focusing. Anal Biochem 85: 331-340.
6. Anderson NL, Anderson NG. 1978b. Analytical techniques for cell fractions. XXII. Two-dimensional analysis of serum and tissue proteins: Multiple gradient-slab gel electrophoresis. Anal Biochem 85: 341-354.
7. Anderson NL, Anderson NG. 2002. The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics 1: 845-867.
8. Anderson NL, Taylor J, Scandora AE, Coulter BP, Anderson NG. 1981. The TYCHO system for computer analysis of two-dimensional gel electrophoresis patterns. Clin Chem 27: 1807-1820.
9. Appel R, Hochstrasser D, Roch C, Funk M, Muller AF, Pellegrini C. 1988. Automatic classification of two-dimensional gel electrophoresis pictures by heuristic clustering analysis: A step toward machine learning. Electrophoresis 9: 136-142.
10. Artoni G, Gianazza E, Zanoni M, Gelfi C, Tanzi MC, Barozzi C, Ferruti P, Righetti PG. 1984. Fractionation techniques in a hydro-organic environment. 2. Acryloyl-morpholine polymers as a matrix for electrophoresis in hydro-organic solvents. Anal Biochem 137: 420-428.
11. Baczek T. 2004a. Fractionation of peptides and identification of proteins from Saccharomyces cerevisiae in proteomics with the use of reversed-phase capillary liquid chromatography and pI-based approach. J Pharm Biomed Anal 35: 895-904.
12. Baczek T. 2004b. Fractionation of peptides in proteomics with the use of pI-based approach and ZipTip pipette tips. J Pharm Biomed Anal 34: 851-860.
13. ell AW, Ward MA, Blackstock WP, Freeman HN, Choudhary JS, Lewis AP, Chotai D, Fazel A, Gushue JN, Paiement J, Palcy S, Chevet E, Lafreniere-Roula M, Solari R, Thomas DY, Rowley A, Bergeron JJ. 2001. Proteomics characterization of abundant Golgi membrane proteins. J Biol Chem 276: 5152-5165.
14. Berggren K, Chernokalskaya E, Steinberg TH, Kemper C, Lopez MF, Diwu Z, Haugland RP, Patton WF. 2000. Background-free, high sensitivity staining of proteins in one-and two-dimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex. Electrophoresis 21: 2509-2521.
15. Bjellqvist B, Hughes GJ, Pasquali C, Paquet N, Ravier F, Sanchez JC, Frutiger S, Hochstrasser D. 1993a. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 14: 1023-1031.
16. Bjellqvist B, Sanchez JC, Pasquali C, Ravier F, Paquet N, Frutiger S, Hughes GJ, Hochstrasser D. 1993b. Micropreparative 2-dimensional electrophoresis allowing the separation of samples containing milligram amounts of proteins. Electrophoresis 14: 1375-1378.
17. Bonner WM, Laskey RA. 1974. A film detection method for tritium-labelled proteins and nucleic acids in polyacrylamide gels. Eur J Biochem 46: 83-88.
18. Braun RJ, Kinkl N, Beer M, Ueffing M. 2007. Two-dimensional electrophoresis of membrane proteins Anal. Bioanal Chem 389: 1033-1045.
19. Bravo R, Celis JE. 1980. A search for differential polypeptide synthesis throughout the cell cycle of HeLa cells. J Cell Biol 84: 795-802.
20. Bravo R, Celis JE. 1982. Human proteins sensitive to neoplastic transformation in cultured epithelial and fibroblast cells. Clin Chem 28: 949-954.
21. Bravo R, Fey SJ, Bellatin J, Larsen PM, Arevalo J, Celis JE. 1981. Identification of a nuclear and of a cytoplasmic polypeptide whose relative proportions are sensitive to changes in the rate of cell proliferation. Exp Cell Res 136: 311-319.
22. Bravo R, Frank R, Blundell PA, Macdonald-Bravo H. 1987. Cyclin/PCNA is the auxiliary protein of DNA polymerase-delta. Nature 326: 515-517.
23. Brown EG. 1988. Mixed anionic detergent/aliphatic alcohol-polyacrylamide gel electrophoresis alters the separation of proteins relative to conventional sodium dodecyl sulfate-polyacrylamidegel electrophoresis. Anal Biochem 174: 337-348.
24. Bunai K, Nozaki M, Hamano M, Ogane S, Inoue T, Nemoto T, Nakanishi H, Yamane K. 2003. Proteomic analysis of acrylamide gel separated proteins immobilized on polyvinylidene difluoride membranes followingproteolytic digestion in the presenceof80%acetonitrile. Proteomics 3: 1738-1749.
25. Bunger MK, Cargile BJ, Sevinsky JR, Deyanova E, Yates NA, Hendrickson RC, Stephenson JL Jr. 2007. Detection and validation of nonsynonymous coding SNPs from orthogonal analysis of shotgun proteomics data. J Proteome Res 6: 2331-2340.
26. Burre J, Beckhaus T, Schagger H, Corvey C, Hofmann S, Karas M, Zimmermann H, Volknandt W. 2006. Analysis of the synaptic vesicle proteome using three gel-based protein separation techniques. Proteomics 6: 6250-6262.
27. Bury AF. 1981. Analysis of protein and peptide mixtures-Evaluation of 3 sodium dodecyl sulfate-polyacrylamide gel-electrophoresis buffer systems. J Chromatogr 213: 491-500.
28. Caglio S, Righetti PG. 1993. On the efficiency of methylene-blue versus persulfate catalysis of polyacrylamide gels, as investigated by capillary zone electrophoresis. Electrophoresis 14: 997-1003. (Pubitemid 23359585)
29. Caglio S, Chiari M, Righetti PG. 1994. Get polymerization in detergents-Conversion efficiency of methylene-blue vs persulfate catalysis, as investigated by capillary zone electrophoresis. Electrophoresis 15: 209-214.
30. Camacho-Carvajal MM, Wollscheid B, Aebersold R, Steimle V, Schamel WWA. 2004. Two-dimensional blue native/SDS gel electrophoresis of multi-protein complexes from whole cellular lysates-A proteomics approach. Mol Cell Proteomics 3: 176-182.
31. Cantin GT, Venable JD, Cociorva D, Yates JR III. 2006. Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway. J Proteome Res 5: 127-134.
32. Cargile BJ, Stephenson JL Jr. 2004. An alternative to tandem mass spectrometry: Isoelectric point and accurate mass for the identification of peptides. Anal Chem 76: 267-275.
33. Cargile BJ, Talley DL, Stephenson JL Jr. 2004. Immobilized pH gradients as a first dimensionin shotgun proteomics and analysis of the accuracy of pI predictability of peptides. Electrophoresis 25: 936-945.
34. Cargile BJ, Sevinsky JR, Essader AS, Eu JP, Stephenson JL Jr. 2008. Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects. Electrophoresis 29: 2768-2778.
35. Castellanos-Serra L, Proenza W, Huerta V, Moritz RL, Simpson RJ. 1999. Proteome analysis of polyacrylamide gel-separated proteins visualized by reversible negative staining using imidazole-zinc salts. Electrophoresis 20: 732-737.
36. Cejka J, Vodrazka Z, Salak J. 1968. Carbamylation of globin in electrophoresis and chromatography in the presence of urea. Biochim Biophys Acta 154: 589-591.
37. Chevallet M, Luche S, Diemer H, Strub JM, Van Dorsselaer A, Rabilloud T. 2008. Sweet silver: Aformaldehyde-free silver staining using aldoses as developing agents, with enhanced compatibility with mass spectrometry. Proteomics 2008 Nov. 10. [Epub ahead of print].
38. Chen J, Gao J, Lee CS. 2003. Dynamic enhancements of sample loading and analyte concentration in capillary isoelectric focusing for proteome studies. J Proteome Res 2: 249-254.
39. Chevalier F, Rofidal V, Vanova P, Bergoin A, Rossignol M. 2004. Proteomic capacity of recent fluorescent dyes for protein staining. Phytochemistry 65: 1499-1506.
40. Chiari M, Righetti PG, Negri A, Ceciliani F, Ronchi S. 1992. Preincubation with cysteine prevents modification of sulfhydryl-groups in proteins by unreacted acrylamide in a gel. Electrophoresis 13: 882-884.
41. Chiari M, Micheletti C, Nesi M, Fazio M, Righetti PG. 1994. Towards new formulations for polyacrylamide matrices-N-Acryloylaminoethoxyethanol, a novel monomer combining high hydrophilicity with extreme hydrolytic stability. Electrophoresis 15: 177-186.
42. Chick JM, Haynes PA, Molloy MP, Bjellqvist B, Baker MS, Len AC. 2008. Characterization of the rat liver membrane proteome using peptide immobilized pH gradient isoelectric focusing. J Proteome Res 7: 1036-1045.
43. Claverol S, Burlet-Schiltz O, Gairin JE, Monsarrat B. 2003. Characterization of protein variants and post-translational modifications: ESI-MSn analyses of intact proteins eluted from polyacrylamide gels. Mol Cell Proteomics 2: 483-493.
44. Cleveland DW, Fischer SG, Kirschner MW, Laemmli UK. 1977. Peptide mapping by limited proteolysis in sodium dodecyl sulfate and analysis by gel electrophoresis. J Biol Chem 252: 1102-1106.
45. Cohen SL, Chait BT. 1997. Mass spectrometry of whole proteins eluted from sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels. Anal Biochem 247: 257-267.
46. Colinge J, Masselot A, Giron M, Dessingy T, Magnin J. 2003. OLAV: Towards high-throughput tandem mass spectrometry data identification. Proteomics 3: 1454-1463.
47. Corbett JM, Dunn MJ, Posch A, Gorg A. 1994. Positional reproducibility of protein spots in two-dimensional polyacrylamide gel electrophoresis using immobilised pH gradient isoelectric focusing in the first dimension: An interlaboratory comparison. Electrophoresis 15: 1205-1211.
48. Coughenour HD, Spaulding RS, Thompson CM. 2004. The synaptic vesicle proteome: A comparative study in membrane protein identification. Proteomics 4: 3141-3155.
49. Courchesne PL, Luethy R, Patterson SD. 1997. Comparison of in-gel and onmembrane digestion methods at low to sub-pmol level for subsequent peptide and fragment-ion mass analysis using matrix-assisted laserdesorption/ionization mass spectrometry. Electrophoresis 18: 369-381.
50. Cox J, Mann M. 2007. Is proteomics the new genomics? Cell 130: 395-398.
51. Daban JR, Aragay AM. 1984. Rapid fluorescent staining of histones in sodium dodecyl sulfate-polyacrylamide gels. Anal Biochem 138: 223-228.
52. Daban JR, Bartolome S, Samso M. 1991. Use of the hydrophobic probe Nile red for the fluorescent staining of protein bands in sodium dodecyl sulfate-polyacrylamide gels. Anal Biochem 199: 169-174.
53. Davis BJ. 1964. Disc electrophoresis. II. Method and application to human serum proteins. Ann NYAcad Sci 121: 404-427.
54. Domon B, Aebersold R. 2006. Challenges and opportunities in proteomics data analysis. Mol Cell Proteomics 5: 1921-1926.
55. Dukan S, Turlin E, Biville F, Bolbach G, Touati D, Tabet JC, Blais JC. 1998. Coupling 2D SDS-PAGE with CNBr cleavage and MALDI-TOFMS: A strategy applied to the identification of proteins induced by a hypochlorous acid stress in Escherichia coli. Anal Chem 70: 4433-4440.
56. Duncan R, McConkey EH. 1982. How many proteins are there in a typical mammalian cell? Clin Chem 28: 749-755.
57. Egen NB, Bliss M, Mayersohn M, Owens SM, Arnold L, Bier M. 1988. Isolation of monoclonal antibodies to phencyclidine from ascites fluid by preparative isoelectric focusing in the Rotofor. Anal Biochem 172: 488-494.
58. Eng JK, McCormack AL, Yates JR. 1994. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database. J Am Soc Mass Spectrom 5: 976-989.
59. Eravci M, Fuxius S, Broedel O, Weist S, Krause E, Stephanowitz H, Schluter H, Eravci S, Baumgartner A. 2008. The whereabouts of transmembrane proteins from rat brain synaptosomes during two-dimensional gel electrophoresis. Proteomics 8: 1762-1770.
60. Essader AS, Cargile BJ, Bundy JL, Stephenson JL Jr. 2005. A comparison of immobilized pH gradient isoelectric focusing and strong-cationexchange chromatography as a first dimension in shotgun proteomics. Proteomics 5: 24-34.
61. Fernandez-Patron C, Castellanos-Serra L, Rodriguez P. 1992. Reverse staining of sodium dodecyl sulfate polyacrylamide gels by imidazolezinc salts: Sensitive detection of unmodified proteins. Biotechniques 12: 564-573.
62. Figeys D, Zhang Y, Aebersold R. 1998. Optimization of solid phase microextraction-Capillary zone electrophoresis-Mass spectrometry for high sensitivity protein identification. Electrophoresis 19: 2338-2347.
63. Fritz JD, Swartz DR, Greaser ML. 1989. Factors affecting polyacrylamide gel electrophoresis and electroblotting of high-molecular-weight myofibrillar proteins. Anal Biochem 180: 205-210.
64. Garrels JI. 1979a. Changes in protein synthesis during myogenesis in a clonal cell line. Dev Biol 73: 134-152.
65. Garrels JI. 1979b. Two dimensional gel electrophoresis and computer analysis of proteins synthesized by clonal cell lines. J Biol Chem 254: 7961-7977.
66. Gelfi C, Righetti PG. 1981a. Polymerization kinetics of polyacrylamide gels. 2. Effect of Temperature. Electrophoresis 2: 220-228.
67. Gelfi C, Righetti PG. 1981b. Polymerization kinetics of polyacrylamide gels. 1. Effect of different cross-linkers. Electrophoresis 2: 213-219.
68. Giometti CS, Barany M, Danon MJ, Anderson NG. 1980. Muscle protein analysis. II. Two-dimensional electrophoresis of normal and diseased human skelet al. muscle. Clin Chem 26: 1152-1155.
69. Gordon JA, Jencks WP. 1963. The relationship of structure to the effectiveness of denaturing agents for proteins. Biochemistry 2: 47-57.
70. Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A. 2005. H++: A server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 33: W368-W371.
71. Gorg A, Postel W, Gunther S. 1988. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 9: 531-546.
72. Gorg A, Obermaier C, Boguth G, Harder A, Scheibe B, Wildgruber R, Weiss W. 2000. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21: 1037-1053.
73. Gorg A, Boguth G, Kopf A, Reil G, Parlar H, Weiss W. 2002. Sample prefractionation with Sephadex isoelectric focusing prior to narrow pH range two-dimensional gels. Proteomics 2: 1652-1657.
74. Groleau PE, Jimenez-Flores R, Gauthier SF, Pouliot Y. 2002. Fractionation of beta-lactoglobulin tryptic peptides by ampholyte-free isoelectric focusing. J Agric Food Chem 50: 578-583.
75. Gronow M, Griffiths G. 1971. Rapid isolation and separation of the nonhistone proteins of rat liver nuclei. FEBS Lett 15: 340-344.
76. Han CL, Chien CW, Chen WC, Chen YR, Wu CP, Li H, Chen YJ. 2008. A multiplexed quantitative strategy for membrane proteomics: Opportunities for mining therapeutic targets for autosomal-dominant polycystic kidney disease. Mol Cell Proteomics 7: 1983-1997.
77. Hardison R, Chalkley R. 1978. Polyacrylamide gel electrophoretic fractionation of histones. Methods Cell Biol 17: 235-251.
78. Hartinger J, Stenius K, Hogemann D, Jahn R. 1996. 16-BAC/SDS-PAGE: A two-dimensional gel electrophoresis system suitable for the separation of integral membrane proteins. Anal Biochem 240: 126-133.
79. Heller M, Ye M, Michel PE, Morier P, Stalder D, Junger MA, Aebersold R, Reymond F, Rossier JS. 2005. Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides. J Proteome Res 4: 2273-2282.
80. Henrich S, Cordwell SJ, Crossett B, Baker MS, Christopherson RI. 2007. The nuclear proteome and DNA-binding fraction of human Raji lymphoma cells. Biochim Biophys Acta 1774: 413-432.
81. Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C, Watanabe C. 1993. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci USA 90: 5011-5015.
82. Hisabori T, Inoue K, Akabane Y, Iwakami S, Manabe K. 1991. Twodimensional gel electrophoresis of the membrane-bound protein complexes, including photosystem I, of thylakoid membranes in the presence of sodium oligooxyethylene alkyl ether sulfate/dimethyl dodecylamine oxide and sodium dodecyl sulfate. J Biochem Biophys Methods 22: 253-260.
83. Hoffert JD, Knepper MA. 2008. Taking aim at shotgun phosphoproteomics. Anal Biochem 375: 1-10.
84. Hoffmann P, Ji H, Moritz RL, Connolly LM, Frecklington DF, Layton MJ, Eddes JS, Simpson RJ. 2001. Continuous free-flow electrophoresis separation of cytosolic proteins from the human colon carcinoma cell line LIM1215: A non two-dimensional gel electrophoresis-based proteome analysis strategy. Proteomics 1: 807-818.
85. Horowitz PM, Bowman S. 1987. Ion-enhanced fluorescence staining of sodium dodecyl sulfate-polyacrylamide gels using bis (8-p-toluidino-1- naphthalenesulfonate). Anal Biochem 165: 430-434.
86. Horth P, Miller CA, Preckel T, Wenz C. 2006. Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis. Mol Cell Proteomics 5: 1968-1974.
87. Hunzinger C, Wozny W, Schwall GP, Poznanovic S, Stegmann W, Zengerling H, Schoepf R, Groebe K, Cahill MA, Osiewacz HD, Jaegemann N, Bloch M, Dencher NA, Krause F, Schrattenholz A. 2006. Comparative profiling of the mammalian mitochondrial proteome: Multiple aconitase-2 iosorms including N-formylkynurenine modifications as part of a protein biomarker signature for reactive oxidative species. J Proteome Res 5: 625-633.
88. James P, Quadroni M, Carafoli E, Gonnet G. 1993. Protein identification by mass profile fingerprinting. Biochem Biophys Res Commun 195: 58-64.
89. Johnson BF. 1982. Enhanced resolution in two-dimensional electrophoresis of low-molecular-weight proteins while utilizing enlarged gels. Anal Biochem 127: 235-246.
90. Johnston RF, Pickett SC, Barker DL. 1990. Autoradiography using storage phosphor technology. Electrophoresis 11: 355-360.
91. Jorgensen CS, Jagd M, Sorensen BK, McGuire J, Barkholt V, Hojrup P, Houen G. 2004. Efficacy and compatibility with mass spectrometry of methods for elution of proteins from sodium dodecyl sulfate-polyacrylamide gels and polyvinyldifluoride membranes. Anal Biochem 330: 87-97.
92. Jovin TM. 1973a. Multiphasic zone electrophoresis. I. Steady-state movingboundary systems formed by different electrolyte combinations. Biochemistry 12: 871-879.
93. Jovin TM. 1973b. Multiphasic zone electrophoresis. II. Design of integrated discontinuous buffer systems for analytical and preparative fractionation. Biochemistry 12: 879-890.
94. Kasicka V. 2008. Recent developments in CE and CEC of peptides. Electrophoresis 29: 179-206.
95. Keller A, Nesvizhskii AI, Kolker E, Aebersold R. 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74: 5383-5392.
96. Kobayashi N. 2004. Recent progress of free-flow electrophoresis method and its application for proteomics. Tanpakushitsu Kakusan Koso 49: 1333-1340.
97. Krijgsveld J, Gauci S, Dormeyer W, Heck AJ. 2006. In-gel isoelectric focusing of peptides as a tool for improved protein identification. J Proteome Res 5: 1721-1730.
98. Krokhin OV. 2006. Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: Application to 300-and 100-A pore size C18 sorbents. Anal Chem 78: 7785-7795.
99. Kuroda Y, Yukinaga H, Kitano M, Noguchi T, Nemati M, Shibukawa A, Nakagawa T, Matsuzaki K. 2005. On-line capillary isoelectric focusingmass spectrometry for quantitative analysis of peptides and proteins. J Pharm Biomed Anal 37: 423-428.
100. Kuster B, Schirle M, Mallick P, Aebersold R. 2005. Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol 6: 577-583.
101. Kyte J, Rodriguez H. 1983. A discontinuous electrophoretic system for separating peptides on polyacrylamide gels. Anal Biochem 133: 515-522.
102. Laemmli UK. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685.
103. Lambert JP, Ethier M, Smith JC, Figeys D. 2005. Proteomics: From gel-based to gel free. Anal Chem 77: 3771-3788.
104. Langen H, Takacs B, Evers S, Berndt P, Lahm HW, Wipf B, Gray C, Fountoulakis M. 2000. Two-dimensional map of the proteome of Haemophilus influenzae. Electrophoresis 21: 411-429.
105. Lasonder E, Ishihama Y, Andersen JS, Vermunt AM, Pain A, Sauerwein RW, Eling WM, Hall N, Waters AP, Stunnenberg HG, Mann M. 2002. Analysis of the plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419: 537-542.
106. Lengqvist J, Uhlen K, Lehtio J. 2007. iTRAQ compatibility of peptide immobilized pH gradient isoelectric focusing. Proteomics 7: 1746-1752.
107. Liang X, Bai J, Liu YH, Lubman DM. 1996. Characterization of SDS-PAGE-separated proteins by matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem 68: 1012-1018.
108. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR III. 1999. Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17: 676-682.
109. Liu H, Sadygov RG, Yates JR III. 2004. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76: 4193-4201.
110. Locke S, Figeys D. 2000. Techniques for the optimization of proteomic strategies based on head column stacking capillary electrophoresis. Anal Chem 72: 2684-2689.
111. Loo RRO, Hayes R, Yang YN, Hung F, Ramachandran P, Kim N, Gunsalus R, Loo JA. 2005. Top-down, bottom-up, and side-to-side proteomics with virtual 2-D gels. Int J Mass Spectrom 240: 317-325.
112. Lopez MF, Patton WF, Utterback BL, Chung-Welch N, Barry P, Skea WM, Cambria RP. 1991. Effect of various detergents on protein migration in the second dimension of two-dimensional gels. Anal Biochem 199: 35-44.
113. Lu X, Zhu H. 2005. Tube-gel digestion: A novel proteomic approach for high throughput analysis of membrane proteins. Mol Cell Proteomics 4: 1948-1958.
114. Lu B, Motoyama A, Ruse C, Venable J, Yates JR III. 2008. Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data. Anal Chem 80: 2018-2025.
115. Lu P, Vogel C, Wang R, Yao X, Marcotte EM. 2007. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 25: 117-124.
116. Luche S, Lelong C, Diemer H, Van Dorsselaer A, Rabilloud T. 2007. Ultrafast coelectrophoretic fluorescent staining of proteins with carbocyanines. Proteomics 7: 3234-3244.
117. Lui M, Tempst P, Erdjument-Bromage H. 1996. Methodical analysis of protein-nitrocellulose interactions to design a refined digestion protocol. Anal Biochem 241: 156-166.
118. Luo S, Wehr NB, Levine RL. 2006. Quantitation of protein on gels and blots by infrared fluorescence of Coomassie blue and Fast Green. Anal Biochem 350: 233-238.
119. Luque-Garcia JL, Zhou G, Sun TT, Neubert TA. 2006. Use of nitrocellulose membranes for protein characterization by matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem 78: 5102-5108.
120. Lyubimova T, Caglio S, Gelfi C, Righetti PG, Rabilloud T. 1993. Photopolymerization of polyacrylamide gels with methylene-blue. Electrophoresis 14: 40-50.
121. Macfarlane DE. 1983. Use of benzyldimethyl-n-hexadecylammonium chloride ("16-BAC"), a cationic detergent, in an acidic polyacrylamide gel electrophoresis system to detect base labile protein methylation in intact cells. Anal Biochem 132: 231-235.
122. Macfarlane DE. 1989. Two dimensional benzyldimethyl-n-hexadecylammonium chloride-Sodium dodecyl sulfate preparative polyacrylamide gel electrophoresis: A high capacity high resolution technique for the purification of proteins from complex mixtures. Anal Biochem 176:457-463.
123. MacGillivray AJ, Rickwood D. 1974. The heterogeneity of mouse-chromatin nonhistone proteins as evidenced by two-dimensional polyacrylamidegel electrophoresis and ion-exchange chromatography. Eur J Biochem 41: 181-190.
124. Mackintosh JA, Choi HY, Bae SH, Veal DA, Bell PJ, Ferrari BC, Van Dyk DD, Verrills NM, Paik YK, Karuso P. 2003. A fluorescent natural product for ultra sensitive detection of proteins in one-dimensional and twodimensional gel electrophoresis. Proteomics 3: 2273-2288.
125. Malmstrom J, Lee H, Nesvizhskii AI, Shteynberg D, Mohanty S, Brunner E, Ye M, Weber G, Eckerskorn C, Aebersold R. 2006. Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. J Proteome Res 5: 2241-2249.
126. Malone JP, Radabaugh MR, Leimgruber RM, Gerstenecker GS. 2001. Practical aspects of fluorescent staining for proteomic applications. Electrophoresis 22: 919-932.
127. Matsudaira P. 1987. Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J Biol Chem 262: 10035-10038.
128. Mazzeo JR, Martineau JA, Krull IS. 1993. Peptide mapping using EOF-driven capillary isoelectric focusing. Anal Biochem 208: 323-329.
129. Mets LJ, Bogorad L. 1974. Two-dimensional polyacrylamide gel electrophoresis: An improved method for ribosomal proteins. Anal Biochem 57: 200-210.
130. Moritz RL, Ji H, Schutz F, Connolly LM, Kapp EA, Speed TP, Simpson RJ. 2004. A proteome strategy for fractionating proteins and peptides using continuous free-flow electrophoresis coupled off-line to reversed-phase high-performance liquid chromatography. Anal Chem 76: 4811-4824.
131. Nakamura K, Okuya Y, Katahira M, Yoshida S, Wada S, Okuno M. 1992. Analysis of tubulin isoforms by two-dimensional gel electrophoresis using SDS-polyacrylamide gel electrophoresis in the first dimension. J Biochem Biophys Methods 24: 195-203.
132. Navarre C, Degand H, Bennett KL, Crawford JS, Mortz E, Boutry M. 2002. Subproteomics: Identification of plasma membrane proteins from the yeast Saccharomyces cerevisiae. Proteomics 2: 1706-1714.
133. Neuhoff V, Arold N, Taube D, Ehrhardt W. 1988. Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250. Electrophoresis 9: 255-262.
134. Nielsen ML, Savitski MM, Zubarev RA. 2006. Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics. Mol Cell Proteomics 5: 2384-2391.
135. Novakova Z, Man P, Novak P, Hozak P, Hodny Z. 2006. Separation of nuclear protein complexes by blue native polyacrylamide gel electrophoresis. Electrophoresis 27: 1277-1287.
136. O'Farrell PH. 1975. High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250: 4007-4021.
137. O'Farrell PZ, Goodman HM, O'Farrell PH. 1977. High resolution twodimensional electrophoresis of basic as well as acidic proteins. Cell 12: 1133-1141.
138. Ogorzalek Loo RR, Mitchell C, Stevenson TI, Martin SA, Hines WM, Juhasz P, Patterson DH, Peltier JM, Loo JA, Andrews PC. 1997. Sensitivity and mass accuracy for proteins analyzed directly from polyacrylamide gels: Implications for proteome mapping. Electrophoresis 18: 382-390.
139. Orrick LR, Olson MO, Busch H. 1973. Comparison of nucleolar proteins of normal rat liver and Novikoff hepatoma ascites cells by twodimensional polyacrylamide gel electrophoresis. Proc Natl Acad Sci USA 70: 1316-1320.
140. Ortiz ML, Calero M, Fernandez Patron C, Patron CF, Castellanos L, Mendez E. 1992. Imidazole-SDS-Zn reverse staining of proteins in gels containing or not SDS and microsequence of individual unmodified electroblotted proteins. FEBS Lett 296: 300-304.
141. Oses-Prieto JA, Zhang X, Burlingame AL. 2007. Formation of epsilonformyllysine on silver-stained proteins: Implications for assignment of isobaric dimethylation sites by tandem mass spectrometry. Mol Cell Proteomics 6: 181-192.
142. Pappin DJ, Hojrup P, Bleasby AJ. 1993. Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol 3: 327-332.
143. Patton WF, Chung-Welch N, Lopez MF, Cambria RP, Utterback BL, Skea WM. 1991. Tris-tricine and Tris-borate buffer systems provide better estimates of human mesothelial cell intermediate filament protein molecular weights than the standard Tris-glycine system. Anal Biochem 197: 25-33.
144. Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP. 2003. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J Proteome Res 2: 43-50.
145. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551-3567.
146. Petritis K, Kangas LJ, Ferguson PL, Anderson GA, Pasa-Tolic L, Lipton MS, Auberry KJ, Strittmatter EF, Shen Y, Zhao R, Smith RD. 2003. Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. Anal Chem 75: 1039-1048.
147. Phelps DS. 1984. Electrophoretic transfer of proteins from fixed and stained gels. Anal Biochem 141: 409-412.
148. Rabilloud T. 1990. Mechanisms of protein silver staining in polyacrylamide gels: A 10-year synthesis. Electrophoresis 11: 785-794.
149. Rabilloud T. 1998. Use of thiourea to increase the solubility of membrane proteins in two-dimensional electrophoresis. Electrophoresis 19: 758-760. (Pubitemid 28236679)
150. Rabilloud T, Strub JM, Luche S, van Dorsselaer A, Lunardi J. 2001. Comparison between Sypro Ruby and ruthenium II tris (bathophenanthroline disulfonate) as fluorescent stains for protein detection in gels. Proteomics 1: 699-704.
151. Rabilloud T, Heller M, Gasnier F, Luche S, Rey C, Aebersold R, Benahmed M, Louisot P, Lunardi J. 2002. Proteomics analysis of cellular response to oxidative stress-Evidence for in vivo overoxidation of peroxiredoxins at their active site. J Biol Chem 277: 19396-19401.
152. Radola BJ. 1973. Isoelectric focusing in layers of granulated gels. I. Thinlayer isoelectric focusing of proteins. Biochim Biophys Acta 295: 412-428.
153. Radola BJ. 1975. Isoelectric focusing in layers of granulated gels. II. Preparative isoelectric focusing. Biochim Biophys Acta 386: 181-195.
154. Rais I, Karas M, Schagger H. 2004. Two-dimensional electrophoresis for the isolation of integral membrane proteins and mass spectrometric identification. Proteomics 4: 2567-2571.
155. Reid GE, Ji H, Eddes JS, Moritz RL, Simpson RJ. 1995. Nonreducing twodimensional polyacrylamide gel electrophoretic analysis of human colonic proteins. Electrophoresis 16: 1120-1130.
156. Reynolds JA, Tanford C. 1970. Binding of dodecyl sulfate to proteins at high binding ratios. Possible implications for the state of proteins in biological membranes. Proc Natl Acad Sci USA 66: 1002-1007.
157. Richert S, Luche S, Chevallet M, Van Dorsselaer A, Leize-Wagner E, Rabilloud T. 2004. About the mechanism of interference of silver staining with peptide mass spectrometry. Proteomics 4: 909-916.
158. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17: 1030-1032.
159. Righetti PG. 1989. Of matrices and men. J Biochem Biophys Methods 19: 1-20.
160. Righetti PG, Caglio S. 1993. On the kinetics of monomer incorporation into polyacrylamide gels, as investigated by capillary zone electrophoresis. Electrophoresis 14: 573-582. (Pubitemid 23257933)
161. Righetti PG, Gianazza E. 1987. Isoelectric focusing in immobilized pH gradients: Theory and newer methodology. Methods Biochem Anal 32: 215-278.
162. Righetti PG, Barzaghi B, Luzzana M, Manfredi G, Faupel M. 1987. A horizontal apparatus for isoelectric protein-purification in a segmented immobilized pH gradient. J Biochem Biophys Methods 15: 189-198. (Pubitemid 18026274)
163. Righetti PG, Castagna A, Herbert B, Candiano G. 2005. How to bring the "unseen" proteome to the limelight via electrophoretic pre-fractionation techniques. Biosci Rep 25: 3-17.
164. Ros A, Faupel M, Mees H, Oostrum J, Ferrigno R, Reymond F, Michel P,
165. Rosengren A, Bjellqvist B, Gasparic V. 1977. Method for generating a pH function for usein electrophoresis. US patent 4130470, 1978, extension of German patent DE2656162, 1977.
166. Rosenfeld J, Capdevielle J, Guillemot JC, Ferrara P. 1992. In-gel digestion of proteins for internal sequence analysis after one-or two-dimensional gel electrophoresis. Anal Biochem 203: 173-179.
167. Sanchez JC, Ravier F, Pasquali C, Frutiger S, Paquet N, Bjellqvist B, Hochstrasser DF, Hughes GJ. 1992. Improving the detection of proteins after transfer to polyvinylidene difluoride membranes. Electrophoresis 13: 715-717.
168. Santoni V, Molloy M, Rabilloud T. 2000. Membrane proteins and proteomics: Un amour impossible? Electrophoresis 21: 1054-1070.
169. Schagger H, von Jagow G. 1987. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem 166: 368-379.
170. Schagger H, von Jagow G. 1991. Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal Biochem 199: 223-231.
171. Scherl A, Francois P, Charbonnier Y, Deshusses JM, Koessler T, Huyghe A, Bento M, Stahl-Zeng J, Fischer A, Masselot A, Vaezzadeh A, Galle F, Renzoni A, Vaudaux P, Lew D, Zimmermann-Ivol CG, Binz PA, Sanchez JC, Hochstrasser DF, Schrenzel J. 2006. Exploring glycopeptide-resistance in Staphylococcus aureus: A combined proteomics and transcriptomics approach for the identification of resistance-related markers. BMC Genomics 7: 296.
172. Schirle M, Heurtier MA, Kuster B. 2003. Profiling core proteomes of human cell lines by one-dimensional PAGE and liquid chromatographytandem mass spectrometry. Mol Cell Proteomics 2: 1297-1305.
173. Schluesener D, Rogner M, Poetsch A. 2007. Evaluation of two proteomics technologies used to screen the membrane proteomes of wild-type Corynebacterium glutamicum and an L-lysine-producing strain. Anal Bioanal Chem 389: 1055-1064.
174. Schmitt LM. 2001. Theory of genetic algorithms. Theor Comput Sci 259: 1-61.
175. Sevinsky JR, Brown KJ, Cargile BJ, Bundy JL, Stephenson JL Jr. 2007. Minimizing back exchange in 18O/16O quantitative proteomics experiments by incorporation of immobilized trypsin into the initial digestion step. Anal Chem 79: 2158-2162.
176. Sevinsky JR, Cargile BJ, Bunger MK, Meng F, Yates NA, Hendrickson RC, Stephenson JL Jr. 2008. Whole genome searching with shotgun proteomic data: Applications for genome annotation. J Proteome Res 7: 80-88.
177. Shang TQ, Ginter JM, Johnston MV, Larsen BS, McEwen CN. 2003. Carrier ampholyte-free solution isoelectric focusing as a prefractionation method for the proteomic analysis of complex protein mixtures. Electrophoresis 24: 2359-2368.
178. Shapiro AL, Vinuela E, Maizel JV Jr. 1967. Molecular weight estimation of polypeptide chains by electrophoresis in SDS-polyacrylamide gels. Biochem Biophys Res Commun 28: 815-820.
179. Shen Y, Berger SJ, Anderson GA, Smith RD. 2000. High-efficiency capillary isoelectric focusing of peptides. Anal Chem 72: 2154-2159. (Pubitemid 30316595)
180. Shimura K, Zhi W, Matsumoto H, Kasai K. 2000. Accuracy in the determination of isoelectric points of some proteins and a peptide by capillary isoelectric focusing: Utility of synthetic peptides as isoelectric point markers. Anal Chem 72: 4747-4757.
181. Shimura K, Kamiya K, Matsumoto H, Kasai K. 2002. Fluorescence-labeled peptide pI markers for capillary isoelectric focusing. Anal Chem 74: 1046-1053. (Pubitemid 34203026)
182. Siemankowski RF, Giambalvo A, Dreizen P. 1978. A new analytical procedure for two-dimensional electrophoresis of cellular proteins: Comparison of protein compositions of parent strain and a K+-accumulation mutant of E. coli. Physiol Chem Phys 10: 415-434.
183. SimoAlfonso E, Gelfi C, Sebastiano R, Citterio A, Righetti PG. 1996. Novel acrylamido monomers with higher hydrophilicity and improved hydrolytic stability. 2. Properties of N-acryloylaminopropanol. Electrophoresis 17: 732-737.
184. Simpson DC, Smith RD. 2005. Combining capillary electrophoresis with mass spectrometry for applications in proteomics. Electrophoresis 26: 1291-1305.
185. Steinberg TH, Haugland RP, Singer VL. 1996. Applications of SYPRO Orange and SYPRO Red protein gel stains. Anal Biochem 239: 238-245.
186. Steinberg TH, Lauber WM, Berggren K, Kemper C, Yue S, Patton WF. 2000. Fluorescence detection of proteins in sodium dodecyl sulfatepolyacrylamide gels using environmentally benign, nonfixative, saline solution. Electrophoresis 21: 497-508.
187. Switzer RC III, Merril CR, Shifrin S. 1979. A highly sensitive silver stain for detecting proteins and peptides in polyacrylamide gels. Anal Biochem 98: 231-237.
188. Szponarski W, Sommerer N, Boyer JC, Rossignol M, Gibrat R. 2004. Largescale characterization of integral proteins from Arabidopsis vacuolar membrane by two-dimensional liquid chromatography. Proteomics 4: 397-406.
189. Szponarski W, Delom F, Sommerer N, Rossignol M, Gibrat R. 2007. Separation, identification, and profiling of membrane proteins by GFC/IEC/SDS-PAGE and MALDI TOF MS. Methods Mol Biol 355: 267-278.
190. Tabb DL, McDonald WH, Yates JR III. 2002. DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res 1: 21-26.
191. Tan A, Pashkova A, Zang L, Foret F, Karger BL. 2002. A miniaturized multichamber solution isoelectric focusing device for separation of protein digests. Electrophoresis 23: 3599-3607.
192. Tarroux P, Vincens P, Rabilloud T. 1987. Hermes-A 2nd generation approach to the automatic-analysis of two-dimensional electrophoresis gels. 5. Data-analysis. Electrophoresis 8: 187-199.
193. Tastet C, Lescuyer P, Diemer H, Luche S, van Dorsselaer A, Rabilloud T. 2003. A versatile electrophoresis system for the analysis of high-and low-molecular-weight proteins. Electrophoresis 24: 1787-1794.
194. Towbin H, Staehelin T, Gordon J. 1979. Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: Procedure and some applications. Proc Natl Acad Sci USA 76: 4350-4354.
195. Tsugita A, Miyazaki K, Nabetani T, Nozawa T, Kamo M, Kawakami T. 2001. Application of chemical selective cleavage methods to analyze posttranslational modification in proteins. Proteomics 1: 1082-1091.
196. Tuszynski GP, Buck CA, Warren L.1979. A two-dimensional polyacrylamide gel electrophoresis (PAGE) system using sodium dodecyl sulfate-PAGE in the first dimension. Anal Biochem 93: 329-338.
197. Unlu M, Morgan ME, Minden JS. 1997. Difference gel electrophoresis: A single gel method for detecting changes in protein extracts. Electrophoresis 18: 2071-2077.
198. van Oostveen I, Ducret A, Aebersold R. 1997. Colloidal silver staining of electroblotted proteins for high sensitivity peptide mapping by liquid chromatography-electrospray ionization tandem mass spectrometry. Anal Biochem 247: 310-318.
199. Vonguyen L, Wu J, Pawliszyn J. 1994. Peptide mapping of bovine and chicken cytochrome c by capillary isoelectric focusing with universal concentration gradient imaging. J Chromatogr B Biomed Appl 657: 333-338.
200. Voris BP, Young DA. 1980. Very-high-resolution two-dimensional gel electrophoresis of proteins using giant gels. Anal Biochem 104: 478-484.
201. Wang Y, Hancock WS, Weber G, Eckerskorn C, Palmer-Toy D. 2004. Free flow electrophoresis coupled with liquid chromatography-mass spectrometry for a proteomic study of the human cell line (K562/CR3). J Chromatogr A 1053: 269-278.
202. Wang W, Guo T, Rudnick PA, Song T, Li J, Zhuang Z, Zheng W, Devoe DL, Lee CS, Balgley BM. 2007. Membrane proteome analysis of microdissected ovarian tumor tissues using capillary isoelectric focusing/reversed-phase liquid chromatography-tandem MS. Anal Chem 79: 1002-1009.
203. Washburn MP, Wolters D, Yates JR. 2001. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19: 242-247. (Pubitemid 32220565)
204. Weber K, Kuter DJ. 1971. Reversible denaturation of enzymes by sodium dodecyl sulfate. J Biol Chem 246: 4504-4509.
205. Wen L, Tweten RK, Isackson PJ, Iandolo JJ, Reeck GR. 1983. Ionic interactions between proteins in nonequilibrium pH gradient electrophoresis: Histones affect the migration of high mobility group nonhistone chromatin proteins. Anal Biochem 132: 294-304.
206. West MHP, Wu RS, Bonner WM. 1984. Polyacrylamide-gel electrophoresis of small peptides. Electrophoresis 5: 133-138.
207. White IR, Pickford R, Wood J, Skehel JM, Gangadharan B, Cutler P. 2004. A statistical comparison of silver and SYPRO Ruby staining for proteomic analysis. Electrophoresis 25: 3048-3054.
208. Wilkins MR, Gasteiger E, Sanchez JC, Bairoch A, Hochstrasser DF. 1998. Two-dimensional gel electrophoresis for proteome projects: The effects of protein hydrophobicity and copy number. Electrophoresis 19: 1501-1505.
209. Williams TI, Combs JC, Thakur AP, Strobel HJ, Lynn BC. 2006. A novel Bicine running buffer system for doubled sodium dodecyl sulfate-Polyacrylamide gel electrophoresis of membrane proteins. Electrophoresis 27: 2984-2995.
210. Wiltfang J, Arold N, Neuhoff V. 1991. A new multiphasic buffer system for sodium dodecyl sulfate-polyacrylamide gel electrophoresis of proteins and peptides with molecular masses 100, 000-1000, and their detection with picomolar sensitivity. Electrophoresis 12: 352-366.
211. Winkler C, Denker K, Wortelkamp S, Sickmann A. 2007. Silver-and Coomassie-staining protocols: Detection limits and compatibility with ESI MS. Electrophoresis 28: 2095-2099.
212. Wise GE, Lin F. 1991. Transfer of silver-stained proteins from polyacrylamide gels to polyvinylidene difluoride membranes. J Biochem Biophys Methods 22: 223-231.
213. Witze ES, Old WM, Resing KA, Ahn NG. 2007. Mapping protein posttranslational modifications with mass spectrometry. Nature Methods 4: 798-806.
214. Xiao Z, Conrads TP, Lucas DA, Janini GM, Schaefer CF, Buetow KH, Issaq HJ, Veenstra TD. 2004. Direct ampholyte-free liquid-phase isoelectric peptide focusing: Application to the human serum proteome. Electrophoresis 25: 128-133.
215. Xie H, Bandhakavi S, Griffin TJ. 2005. Evaluating preparative isoelectric focusing of complex peptide mixtures for tandem mass spectrometrybased proteomics: A case study in profiling chromatin-enriched subcellular fractions in Saccharomyces cerevisiae. Anal Chem 77: 3198-3207.
216. Xie H, Bandhakavi S, Roe MR, Griffin TJ. 2007. Preparative peptide isoelectric focusing as a tool for improving the identification of lysineacetylated peptides from complex mixtures. J Proteome Res 6: 2019-2026.
217. Yamaguchi Y, Miyagi Y, Baba H. 2008a. Two-dimensional electrophoresis with cationic detergents: A powerful tool for the proteomic analysis of myelin proteins. Part 1: Technical aspects of electrophoresis. J Neurosci Res 86: 755-765. (Pubitemid 351357757)
218. Yamaguchi Y, Miyagi Y, Baba H. 2008b. Two-dimensional electrophoresis with cationic detergents: A powerful tool for the proteomic analysis of myelin proteins. Part2:Analytical aspects. J Neurosci Res 86: 766-775. (Pubitemid 351357758)
219. Yata M, Sato K, Ohtsuki K, Kawabata M. 1996. Fractionation of peptides in protease digests of proteins by preparative isoelectric focusing in the absence of added ampholyte: A biocompatible and low-cost approach referred to as autofocusing. J Agric Food Chem 44: 76-79.
220. Yates JR III, Speicher S, Griffin PR, Hunkapiller T. 1993. Peptide mass maps: A highly informative approach to protein identification. Anal Biochem 214: 397-408.
221. Young DA. 1984. Advantages of separations on "giant" two-dimensional gels for detection of physiologically relevant changes in the expression of protein gene-products. Clin Chem 30: 2104-2108.
222. Yu W, Li Y, Deng C, Zhang X. 2006. Comprehensive two-dimensional separation in coupling of reversed-phase chromatography with capillary isoelectric focusing followed by MALDI-MS identification using on-target digestion for intact protein analysis. Electrophoresis 27: 2100-2110.
223. Yuan X, Kuramitsu Y, Furumoto H, Zhang X, Hayashi E, Fujimoto M, Nakamura K. 2007. Nuclear protein profiling of Jurkat cells during heat stress-induced apoptosis by 2-DE and MS/MS. Electrophoresis 28: 2018-2026.
224. Zahedi RP, Meisinger C, Sickmann A. 2005. Two-dimensional benzyldimethyl-n-hexadecylammonium chloride/SDS-PAGE for membrane proteomics. Proteomics 5: 3581-3588.
225. Zewert T, Harrington M. 1992. Polyethyleneglycol methacrylate 200 as an electrophoresis matrix in hydroorganic solvents. Electrophoresis 13: 824-831.
226. Zischka H, Weber G, Weber PJ, Posch A, Braun RJ, Buhringer D, Schneider U, Nissum M, Meitinger T, Ueffing M, Eckerskorn C. 2003. Improved proteome analysis of Saccharomyces cerevisiae mitochondria by freeflow electrophoresis. Proteomics 3: 906-916.
227. Zuo X, Speicher DW. 2000. A method for global analysis of complex proteomes using sample prefractionation by solution isoelectrofocusing prior to two-dimensional electrophoresis. Anal Biochem 284: 266-278.