Chapter 40 Identification and Quantification of Protein Posttranslational Modifications

Methods in Enzymology

Volumn 463, Issue C, 2009, Pages 725-763

  Farley, Adam R ^a   Link, Andrew J ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PHOSPHOSERINE; PROTEIN;

ACETYLATION; COLLISIONALLY ACTIVATED DISSOCIATION; COVALENT BOND; ELECTRON TRANSPORT; GLYCOSYLATION; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NITROSATION; OXIDATIVE STRESS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN METHYLATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PURIFICATION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; SIGNAL TRANSDUCTION; SUMOYLATION; TANDEM MASS SPECTROMETRY; UBIQUITINATION; ANIMAL; BIOLOGICAL MODEL; HUMAN; METABOLISM; METHODOLOGY; PHYSIOLOGY;

ANIMALS; HUMANS; MASS SPECTROMETRY; MODELS, BIOLOGICAL; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOMICS;

EID: 71549136813     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(09)63040-8     Document Type: Chapter

References (183)

1. Ahmad I., Hoessli D.C., Walker-Nasir E., Choudhary M.I., Rafik S.M., and Shakoori A.R. J. Cell. Biochem. 99 (2006) 706-718
2. Anderson N.L., and Anderson N.G. Electrophoresis 19 (1998) 1853-1861
3. Armirotti A., Benatti U., and Damonte G. Rapid Commun. Mass Spectrom. 23 (2009) 661-666
4. Bantscheff M., Schirle M., Sweetman G., Rick J., and Kuster B. Anal. Bioanal. Chem. 389 (2007) 1017-1031
5. Bantscheff M., Boesche M., Eberhard D., Matthieson T., Sweetman G., and Kuster B. Mol. Cell. Proteomics 7 (2008) 1702-1713
6. Barnes P.J., Shapiro S.D., and Pauwels R.A. Eur. Respir. J. 22 (2003) 672-688
7. Bayer P., Arndt A., Metzger S., Mahajan R., Melchior F., Jaenicke R., and Becker J. J. Mol. Biol. 280 (1998) 275-286
8. Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., and Gygi S.P. Proc. Natl. Acad. Sci. USA 101 (2004) 12130-12135
9. Beckman J.S., Beckman T.W., Chen J., Marshall P.A., and Freeman B.A. Proc. Natl. Acad. Sci. USA 87 (1990) 1620-1624
10. Bennett K.L., Stensballe A., Podtelejnikov A.V., Moniatte M., and Jensen O.N. J. Mass Spectrom. 37 (2002) 179-190
11. Berger S.L. Nature 447 (2007) 407-412
12. Bernstein E., and Allis C.D. Genes Dev. 19 (2005) 1635-1655
13. Blagoev B., Ong S.E., Kratchmarova I., and Mann M. Nat. Biotechnol. 22 (2004) 1139-1145
14. Blume-Jensen P., and Hunter T. Nature 411 (2001) 355-365
15. Bodenmiller B., Mueller L.N., et al. Nat. Methods 4 (2007) 231-237
16. Bottari P., Aebersold R., et al. Bioconjug. Chem. 15 (2004) 380-388
17. Bunger M.K., Cargile B.J., et al. Anal. Chem. 80 (2008) 1459-1467
18. Cantin G.T., Shock T.R., Park S.K., Madhani H.D., and Yates III J.R. Anal. Chem. 79 (2007) 4666-4673
19. Carr S.A., Huddleston M.J., and Annan R.S. Anal. Biochem. 239 (1996) 180-192
20. Chalkley R.J., Baker P.R., Medzihradszky K.F., Lynn A.J., and Burlingame A.L. Mol. Cell. Proteomics 7 (2008) 2386-2398
21. Chang I.F. Proteomics 6 (2006) 6158-6166
22. Chen Y.R., Chen C.L., Chen W., Zweier J.L., Augusto O., Radi R., and Mason R.P. J. Biol. Chem. 279 (2004) 18054-18062
23. Cirulli C., Chiappetta G., Marino G., Mauri P., and Amoresano A. Anal. Bioanal. Chem. 392 (2008) 147-159
24. Clauser K.R., Baker P., and Burlingame A.L. Anal. Chem. 71 (1999) 2871-2882
25. Cohen P. Eur. J. Biochem. 268 (2001) 5001-5010
26. Collier T.S., Hawkridge A.M., Georgianna D.R., Payne G.A., and Muddiman D.C. Anal. Chem. 80 (2008) 4994-5001
27. Coon J.J., Syka J.E.P., Schwartz J.C., Shabanowitz J., and Hunt D.F. Int. J. Mass Spectrom. 236 (2004) 33-42
28. Coon J.J., Ueberheide B., et al. Proc. Natl. Acad. Sci. USA 102 (2005) 9463-9468
29. Covey T.R., Huang E.C., and Henion J.D. Anal. Chem. 63 (1991) 1193-1200
30. Creasy D.M., and Cottrell J.S. Proteomics 4 (2004) 1534-1536
31. Cunningham Jr. C., Glish G.L., and Burinsky D.J. J. Am. Soc. Mass Spectrom. 17 (2006) 81-84
32. Denison C., Kirkpatrick D.S., and Gygi S.P. Curr. Opin. Chem. Biol. 9 (2005) 69-75
33. Dongre A.R., Jones J.L., Somogyi A., and Wysocki V.H. J. Am. Chem. Soc. 118 (1996) 8365-8374
34. Du Y., Parks B.A., Sohn S., Kwast K.E., and Kelleher N.L. Anal. Chem. 78 (2006) 686-694
35. Durand G., and Seta N. Clin. Chem. 46 (2000) 795-805
36. Fang S., and Weissman A.M. Cell. Mol. Life Sci. 61 (2004) 1546-1561
37. Ferguson J.T., Wenger C.D., Metcalf W.W., and Kelleher N.L. J. Am. Soc. Mass Spectrom. 20 (2009) 1743-1750
38. Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., and White F.M. Nat. Biotechnol. 20 (2002) 301-305
39. Fuchs S.M., Laribee R.N., and Strahl B.D. Biochim. Biophys. Acta 1789 (2009) 26-36
40. Garcia B.A., Shabanowitz J., and Hunt D.F. Methods 35 (2005) 256-264
41. Garcia B.A., Shabanowitz J., and Hunt D.F. Curr. Opin. Chem. Biol. 11 (2007) 66-73
42. Gatzka M., and Walsh C.M. Autoimmunity 40 (2007) 442-452
43. Ge Y., Lawhorn B.G., et al. J. Am. Chem. Soc. 124 (2002) 672-678
44. Ge Y., Rajkumar L., Guzman R.C., Nandi S., Patton W.F., and Agnew B.J. Proteomics 4 (2004) 3464-3467
45. Ge Y., Rybakova I.N., Xu Q., and Moss R.L. Proc. Natl. Acad. Sci. USA 106 (2009) 12658-12663
46. Gerber S.A., Rush J., Stemman O., Kirschner M.W., and Gygi S.P. Proc. Natl. Acad. Sci. USA 100 (2003) 6940-6945
47. Gingras A.C., Raught B., Gygi S.P., Niedzwiecka A., Miron M., Burley S.K., Polakiewicz R.D., Wyslouch-Cieszynska A., Aebersold R., and Sonenberg N. Genes Dev. 15 (2001) 2852-2864
48. Glozak M.A., Sengupta N., Zhang X., and Seto E. Gene 363 (2005) 15-23
49. Godde J.S., and Ura K. J. Biochem. 143 (2008) 287-293
50. Good D.M., Wirtala M., McAlister G.C., and Coon J.J. Mol. Cell. Proteomics 6 (2007) 1942-1951
51. Goodlett D.R., Keller A., Watts J.D., Newitt R., Yi E.C., Purvine S., Eng J.K., von Haller P., Aebersold R., and Kolker E. Rapid Commun. Mass Spectrom. 15 (2001) 1214-1221
52. Goshe M.B., Conrads T.P., Panisko E.A., Angell N.H., Veenstra T.D., and Smith R.D. Anal. Chem. 73 (2001) 2578-2586
53. Grewal S.I., and Rice J.C. Curr. Opin. Cell Biol. 16 (2004) 230-238
54. Griffin T.J., Xie H., Bandhakavi S., Popko J., Mohan A., Carlis J.V., and Higgins L. J. Proteome Res. 6 (2007) 4200-4209
55. Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., and Jensen O.N. Mol. Cell. Proteomics 4 (2005) 310-327
56. Gu W., and Roeder R.G. Cell 90 (1997) 595-606
57. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. Nat. Biotechnol. 17 (1999) 994-999
58. Haas W., Faherty B.K., Gerber S.A., Elias J.E., Beausoleil S.A., Bakalarski C.E., Li X., Villen J., and Gygi S.P. Mol. Cell. Proteomics 5 (2006) 1326-1337
59. Hansen B.T., Jones J.A., Mason D.E., and Liebler D.C. Anal. Chem. 73 (2001) 1676-1683
60. Hansen B.T., Davey S.W., Ham A.J., and Liebler D.C. J. Proteome Res. 4 (2005) 358-368
61. Hayduk E.J., Choe L.H., and Lee K.H. Electrophoresis 25 (2004) 2545-2556
62. Holt G.D., and Hart G.W. J. Biol. Chem. 261 (1986) 8049-8057
63. Huang Y., Triscari J.M., Tseng G.C., Pasa-Tolic L., Lipton M.S., Smith R.D., and Wysocki V.H. Anal. Chem. 77 (2005) 5800-5813
64. Hubbard M.J., and Cohen P. Trends Biochem. Sci. 18 (1993) 172-177
65. Ikeda F., and Dikic I. EMBO Rep. 9 (2008) 536-542
66. Issad T., and Kuo M. Trends Endocrinol. Metab. 19 (2008) 380-389
67. Ito S., Hayama K., and Hirabayashi J. Methods Mol. Biol. 534 (2009) 195-203
68. Jenuwein T., and Allis C.D. Science 293 (2001) 1074-1080
69. Kelleher N.L., Lin H.Y., Valaskovic G.A., Aaserud D.J., Fridriksson E.K., and McLafferty F.W. J. Am. Chem. Soc. 121 (1999) 806-812
70. Kirkpatrick D.S., Denison C., and Gygi S.P. Nat. Cell Biol. 7 (2005) 750-757
71. Lange V., Picotti P., Domon B., and Aebersold R. Mol. Syst. Biol. 4 (2008) 222
72. Larsen M.R., Sorensen G.L., Fey S.J., Larsen P.M., and Roepstorff P. Proteomics 1 (2001) 223-238
73. Larsen M.R., Thingholm T.E., Jensen O.N., Roepstorff P., and Jorgensen T.J. Mol. Cell. Proteomics 4 (2005) 873-886
74. Lee C.H., McComb M.E., Bromirski M., Jilkine A., Ens W., Standing K.G., and Perreault H. Rapid Commun. Mass Spectrom. 15 (2001) 191-202
75. Lim K.B., and Kassel D.B. Anal. Biochem. 354 (2006) 213-219
76. Lochnit G., and Geyer R. Biomed. Chromatogr. 18 (2004) 841-848
77. Lu B., Motoyama A., Ruse C., Venable J., and Yates III J.R. Anal. Chem. 80 (2008) 2018-2025
78. Ma Y., Lu Y., Zeng H., Ron D., Mo W., and Neubert T.A. Rapid Commun. Mass Spectrom. 15 (2001) 1693-1700
79. MacCoss M.J., McDonald W.H., Saraf A., Sadygov R., Clark J.M., Tasto J.J., Gould K.L., Wolters D., Washburn M., Weiss A., Clark J.I., and Yates III J.R. Proc. Natl. Acad. Sci. USA 99 (2002) 7900-7905
80. Macek B., Waanders L.F., Olsen J.V., and Mann M. Mol. Cell. Proteomics 5 (2006) 949-958
81. Makarov A. Anal. Chem. 72 (2000) 1156-1162
82. Makarov A., Denisov E., Kholomeev A., Balschun W., Lange O., Strupat K., and Horning S. Anal. Chem. 78 (2006) 2113-2120
83. Mann M., and Kelleher N.L. Proc. Natl. Acad. Sci. USA 105 (2008) 18132-18138
84. Manza L.L., Codreanu S.G., Stamer S.L., Smith D.L., Wells K.S., Roberts R.L., and Liebler D.C. Chem. Res. Toxicol. 17 (2004) 1706-1715
85. McAlister G.C., Berggren W.T., et al. J. Proteome. Res. 7 (2008) 3127-3136
86. McAlister G.C., Phanstiel D., et al. Anal. Chem. 79 (2007) 3525-3534
87. McLachlin D.T., and Chait B.T. Curr. Opin. Chem. Biol. 5 (2001) 591-602
88. McLachlin D.T., and Chait B.T. Anal. Chem. 75 (2003) 6826-6836
89. Mechref Y., Madera M., and Novotny M.V. Methods Mol. Biol. 424 (2008) 373-396
90. Medzihradszky K.F. Methods Enzymol. 405 (2005) 116-138
91. Medzihradszky K.F., Campbell J.M., Baldwin M.A., Falick A.M., Juhasz P., Vestal M.L., and Burlingame A.L. Anal. Chem. 72 (2000) 552-558
92. Melchior F., Schergaut M., and Pichler A. Trends Biochem. Sci. 28 (2003) 612-618
93. Meng F., Cargile B.J., Patrie S.M., Johnson J.R., McLoughlin S.M., and Kelleher N.L. Anal. Chem. 74 (2002) 2923-2929
94. Mikesh L.M., Ueberheide B., Chi A., Coon J.J., Syka J.E., Shabanowitz J., and Hunt D.F. Biochim. Biophys. Acta 1764 (2006) 1811-1822
95. Miyagi M., and Rao K.C. Mass Spectrom. Rev. 26 (2007) 121-136
96. Oda Y., Huang K., Cross F.R., Cowburn D., and Chait B.T. Proc. Natl. Acad. Sci. USA 96 (1999) 6591-6596
97. Oda Y., Nagasu T., and Chait B.T. Nat. Biotechnol. 19 (2001) 379-382
98. Old W.M., Meyer-Arendt K., Aveline-Wolf L., Pierce K.G., Mendoza A., Sevinsky J.R., Resing K.A., and Ahn N.G. Mol. Cell. Proteomics 4 (2005) 1487-1502
99. Olsen J.V., and Mann M. Proc. Natl. Acad. Sci. USA 101 (2004) 13417-13422
100. Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., and Mann M. Cell 127 (2006) 635-648
101. Olsson A., Manzl C., Strasser A., and Villunger A. Cell Death Differ. 14 (2007) 1561-1575
102. Ong S.E., and Mann M. Nat. Chem. Biol. 1 (2005) 252-262
103. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., and Mann M. Mol. Cell. Proteomics 1 (2002) 376-386
104. Ong S.E., Mittler G., and Mann M. Nat. Methods 1 (2004) 119-126
105. Pan C., Gnad F., Olsen J.V., and Mann M. Proteomics 8 (2008) 4534-4546
106. Paoletti A.C., and Washburn M.P. Biotechnol. Genet. Eng. Rev. 22 (2006) 1-19
107. Parks B.A., Jiang L., Thomas P.M., Wenger C.D., Roth M.J., Boyne II M.T., Burke P.V., Kwast K.E., and Kelleher N.L. Anal. Chem. 79 (2007) 7984-7991
108. Patton W.F. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 771 (2002) 3-31
109. Pedrioli P.G., Raught B., Zhang X.D., Rogers R., Aitchison J., Matunis M., and Aebersold R. Nat. Methods 3 (2006) 533-539
110. Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., and Gygi S.P. Nat. Biotechnol. 21 (2003) 921-926
111. Pflieger D., Junger M.A., Muller M., Rinner O., Lee H., Gehrig P.M., Gstaiger M., and Aebersold R. Mol. Cell. Proteomics 7 (2008) 326-346
112. Pickart C.M., and Fushman D. Curr. Opin. Chem. Biol. 8 (2004) 610-616
113. Pinkse M.W., Uitto P.M., Hilhorst M.J., Ooms B., and Heck A.J. Anal. Chem. 76 (2004) 3935-3943
114. Pitteri S.J., Chrisman P.A., Hogan J.M., and McLuckey S.A. Anal. Chem. 77 (2005) 1831-1839
115. Pless D.D., and Lennarz W.J. Proc. Natl. Acad. Sci. USA 74 (1977) 134-138
116. Polevoda B., and Sherman F. J. Biol. Chem. 275 (2000) 36479-36482
117. Ramos-Fernandez A., Lopez-Ferrer D., and Vazquez J. Mol. Cell. Proteomics 6 (2007) 1274-1286
118. Rao K.C., Palamalai V., Dunlevy J.R., and Miyagi M. Mol. Cell. Proteomics 4 (2005) 1550-1557
119. Reid G., Gallais R., and Metivier R. Int. J. Biochem. Cell Biol. 41 (2009) 155-163
120. Rodriguez M.S., Dargemont C., and Hay R.T. J. Biol. Chem. 276 (2001) 12654-12659
121. Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., Khainovski N., Pillai S., Dey S., Daniels S., Purkayastha S., Juhasz P., et al. Mol. Cell. Proteomics 3 (2004) 1154-1169
122. Roth S.Y., Denu J.M., and Allis C.D. Annu. Rev. Biochem. 70 (2001) 81-120
123. Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.M., Polakiewicz R.D., and Comb M.J. Nat. Biotechnol. 23 (2005) 94-101
124. Sadoul K., Boyault C., Pabion M., and Khochbin S. Biochimie 90 (2008) 306-312
125. Schmidt A., Kellermann J., and Lottspeich F. Proteomics 5 (2005) 4-15
126. Schroeder M.J., Shabanowitz J., Schwartz J.C., Hunt D.F., and Coon J.J. Anal. Chem. 76 (2004) 3590-3598
127. Schulenberg B., Aggeler R., Beechem J.M., Capaldi R.A., and Patton W.F. J. Biol. Chem. 278 (2003) 27251-27255
128. Schulenberg B., Beechem J.M., and Patton W.F. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 793 (2003) 127-139
129. Schulenberg B., Goodman T.N., Aggeler R., Capaldi R.A., and Patton W.F. Electrophoresis 25 (2004) 2526-2532
130. Scigelova M., and Makarov A. Proteomics 6 Suppl. 2 (2006) 16-21
131. Sirard J.C., Vignal C., Dessein R., and Chamaillard M. PLoS Pathog. 3 (2007) e152
132. Siuti N., and Kelleher N.L. Nat. Methods 4 (2007) 817-821
133. Siuti N., Roth M.J., Mizzen C.A., Kelleher N.L., and Pesavento J.J. J. Proteome Res. 5 (2006) 233-239
134. Sliter D.A., Kubota K., Kirkpatrick D.S., Alzayady K.J., Gygi S.P., and Wojcikiewicz R.J. J. Biol. Chem. 283 (2008) 35319-35328
135. Sobel R.E., Cook R.G., and Allis C.D. J. Biol. Chem. 269 (1994) 18576-18582
136. Sokolovsky M., Riordan J.F., and Vallee B.L. Biochem. Biophys. Res. Commun. 27 (1967) 20-25
137. Soufi B., Gnad F., Jensen P.R., Petranovic D., Mann M., Mijakovic I., and Macek B. Proteomics 8 (2008) 3486-3493
138. Spiro R.G. Glycobiology 12 (2002) 43R-56R
139. Steen H., Jebanathirajah J.A., et al. Mol. Cell Proteomics 5 (2006) 172-181
140. Steinberg T.H., Pretty On Top K., Berggren K.N., Kemper C., Jones L., Diwu Z., Haugland R.P., and Patton W.F. Proteomics 1 (2001) 841-855
141. Steinberg T.H., Agnew B.J., Gee K.R., Leung W.Y., Goodman T., Schulenberg B., Hendrickson J., Beechem J.M., Haugland R.P., and Patton W.F. Proteomics 3 (2003) 1128-1144
142. Stemmann O., Zou H., Gerber S.A., Gygi S.P., and Kirschner M.W. Cell 107 (2001) 715-726
143. Strahl B.D., and Allis C.D. Nature 403 (2000) 41-45
144. Swaney D.L., McAlister G.C., and Coon J.J. Nat. Methods 5 (2008) 959-964
145. Swaney D.L., McAlister G.C., Wirtala M., Schwartz J.C., Syka J.E., and Coon J.J. Anal. Chem. 79 (2007) 477-485
146. Syka J.E., Coon J.J., Schroeder M.J., Shabanowitz J., and Hunt D.F. Proc. Natl. Acad. Sci. USA 101 (2004) 9528-9533
147. Sykora C., Hoffmann R., and Hoffmann P. Protein Pept. Lett. 14 (2007) 489-496
148. Tagwerker C., Flick K., Cui M., Guerrero C., Dou Y., Auer B., Baldi P., Huang L., and Kaiser P. Mol. Cell. Proteomics 5 (2006) 737-748
149. Tang W.H., Halpern B.R., Shilov I.V., Seymour S.L., Keating S.P., Loboda A., Patel A.A., Schaeffer D.A., and Nuwaysir L.M. Anal. Chem. 77 (2005) 3931-3946
150. Taniguchi C.M., Emanuelli B., and Kahn C.R. Nat. Rev. Mol. Cell. Biol. 7 (2006) 85-96
151. Tao W.A., Wollscheid B., O'Brien R., Eng J.K., Li X.J., Bodenmiller B., Watts J.D., Hood L., and Aebersold R. Nat. Methods 2 (2005) 591-598
152. Thingholm T.E., Jorgensen T.J., Jensen O.N., and Larsen M.R. Nat. Protoc. 1 (2006) 1929-1935
153. Thompson A., Schafer J., Kuhn K., Kienle S., Schwarz J., Schmidt G., Neumann T., Johnstone R., Mohammed A.K., and Hamon C. Anal. Chem. 75 (2003) 1895-1904
154. Tian Y., Zhou Y., Elliott S., Aebersold R., and Zhang H. Nat. Protoc. 2 (2007) 334-339
155. Trelle M.B., and Jensen O.N. Expert Rev. Proteomics 4 (2007) 491-503
156. Tsaprailis G., Nair H., Somogyi A., Wysocki V.H., Zhong W., Futrell J.H., Summerfield S.G., and Gaskell S.J. J. Am. Chem. Soc. 121 (1999) 5142-5154
157. Udeshi N.D., Shabanowitz J., Hunt D.F., and Rose K.L. FEBS J. 274 (2007) 6269-6276
158. Ulintz P.J., Yocum A.K., Bodenmiller B., Aebersold R., Andrews P.C., and Nesvizhskii A.I. J. Proteome Res. 8 (2009) 887-899
159. Unwin R.D., Griffiths J.R., Leverentz M.K., Grallert A., Hagan I.M., and Whetton A.D. Mol. Cell. Proteomics 4 (2005) 1134-1144
160. Unwin R.D., Griffiths J.R., and Whetton A.D. Nat. Protoc. 4 (2009) 870-877
161. Vestal M.L., and Campbell J.M. Methods Enzymol. 402 (2005) 79-108
162. Waanders L.F., Hanke S., and Mann M. J. Am. Soc. Mass Spectrom. 18 (2007) 2058-2064
163. Washburn M.P., Wolters D., and Yates III J.R. Nat. Biotechnol. 19 (2001) 242-247
164. Wells L., Vosseller K., et al. Mol. Cell Proteomics 1 (2002) 791-804
165. White F.M. Curr. Opin. Biotechnol. 19 (2008) 404-409
166. Williamson B.L., Marchese J., and Morrice N.A. Mol. Cell Proteomics 5 (2006) 337-346
167. Witze E.S., Old W.M., Resing K.A., and Ahn N.G. Nat. Methods 4 (2007) 798-806
168. Wolf-Yadlin A., Hautaniemi S., Lauffenburger D.A., and White F.M. Proc. Natl. Acad. Sci. USA 104 (2007) 5860-5865
169. Wu S.L., Jardine I., et al. Rapid Commun. Mass Spectrom. 18 (2004) 2201-2207
170. Wu C.C., MacCoss M.J., Howell K.E., and Yates III J.R. Nat. Biotechnol. 21 (2003) 532-538
171. Yang Z., and Hancock W.S. J. Chromatogr. A 1070 (2005) 57-64
172. Yang X.J., and Seto E. Mol. Cell. 31 (2008) 449-461
173. Yeo W.S., Lee S.J., Lee J.R., and Kim K.P. BMB Rep. 41 (2008) 194-203
174. Zabrouskov V., Senko M.W., et al. J. Am. Soc Mass Spectrom. 16 (2005) 2027-2038
175. Zappacosta F., Collingwood T.S., Huddleston M.J., and Annan R.S. Mol. Cell. Proteomics 5 (2006) 2019-2030
176. Zhan X., and Desiderio D.M. Biochem. Biophys. Res. Commun. 325 (2004) 1180-1186
177. Zhang R., and Regnier F.E. J. Proteome Res. 1 (2002) 139-147
178. Zhang X., Herring C.J., Romano P.R., Szczepanowska J., Brzeska H., Hinnebusch A.G., and Qin J. Anal. Chem. 70 (1998) 2050-2059
179. Zhang K., Williams K.E., Huang L., Yau P., Siino J.S., Bradbury E.M., Jones P.R., Minch M.J., and Burlingame A.L. Mol. Cell. Proteomics 1 (2002) 500-508
180. Zhang H., Li X.J., Martin D.B., and Aebersold R. Nat. Biotechnol. 21 (2003) 660-666
181. Zhang K., Yau P.M., Chandrasekhar B., New R., Kondrat R., Imai B.S., and Bradbury M.E. Proteomics 4 (2004) 1-10
182. Zhang Y., Wolf-Yadlin A., Ross P.L., Pappin D.J., Rush J., Lauffenburger D.A., and White F.M. Mol. Cell. Proteomics 4 (2005) 1240-1250
183. Zhen Y., Xu N., Richardson B., Becklin R., Savage J.R., Blake K., and Peltier J.M. J. Am. Soc. Mass Spectrom. 15 (2004) 803-822