Biological Mass Spectrometry: Basics and Drug Discovery Related Approaches

Proteomics in Drug Research

Volumn , Issue , 2006, Pages 57-88

  Warscheid, Bettina ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

Biological mass spectrometry; Chemical labeling approaches; Ionization principles; Mass spectrometric instrumentation; Metabolic labeling approaches; Protein identification strategies; Quantitative MS for deciphering protein protein interactions

Indexed keywords

CYTOLOGY; DRUG PRODUCTS; MASS SPECTROMETRY; MOLECULAR BIOLOGY;

BIOLOGICAL MASS SPECTROMETRY; CHEMICAL LABELING; MASS SPECTROMETRIC INSTRUMENTATION; METABOLIC LABELING; PROTEIN IDENTIFICATION; PROTEIN-PROTEIN INTERACTIONS;

PROTEINS;

EID: 67650246523     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/3527608230.ch4     Document Type: Chapter

References (125)

1. Aebersold, R., Rist, B., Gygi, S. P. (2000). Quantitative proteome analysis: methods and applications. Ann. N.Y. Acad. Sci. 919, 33-47.
2. Amanchy, R., Kalume, D. E., Pandey, A. (2005). Stable isotope labeling with amino acids in cell culture (SILAC) for studying dynamics of protein abundance and posttranslational modifications. Sci. STKE 267, 12.
3. Banks, J. F. Jr. (1996). High-sensitivity peptide mapping using packed-capillary liquid chromatography and electrospray ionization mass spectrometry. J. Chrom. A 743, 99-104.
4. Barber, M., Bordoli, R. S., Sedgewick, R. D. and Tyler, A. N. (1981). Fast-atom bombardment of solids (F. A. B.): a new ion source for mass spectrometry. J. Chem. Soc. Chem. Commun. 293, 325-327.
5. Bauer, A., Kuster, B. (2003). Affinity purification-mass spectrometry. Powerful tools for the characterization of protein complexes. Eur. J. Biochem. 270, 570-578.
6. Berhane, B. T., Limbach, P. A. (2003). Stable isotope labeling for matrix-assisted laser desorption/ionization mass spectrometry and post-source decay analysis of ribonucleic acids. J. Mass Spectrom. 38, 872-878.
7. Blagoev, B., Kratchmarova, I., Ong, S. E., Nielsen, M., Foster, L. J., Mann, M. (2003). A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 21, 315-318.
8. Blagoev, B., Ong, S. E., Kratchmarova, I., Mann, M. (2004). Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol. 22, 1139-1145.
9. Blonder, J., Hale, M. L., Chan, K. C., Yu, L. R., Lucas, D. A., Conrads, T. P., Zhou, M., Popoff, M. R., Issaq, H. J., Stiles, B. G., Veenstra, T. D. (2005). Quantitative profiling of the detergent-resistant membrane proteome of iota-b toxin induced vero cells. J. Proteome Res. 4, 523-531.
10. Bonenfant, D., Schmelzle, T., Jacinto, E., Crespo, J. L., Mini, T., Hall, M. N., Jenoe, P. (2003). Quantification of changes in protein phosphorylation: a simple method based on stable isotope labeling and mass spectrometry. Proc. Natl. Acad. Sci. USA 100, 880-885.
11. Brand, M., Ranish, J. A., Kummer, N. T., Hamilton, J., Igarashi, K., Francastel, C., Chi, T. H., Crabtree, G. R., Aebersold, R., Groudine, M. (2004). Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat. Struct. Mol. Biol. 11, 73-80.
12. Brown, K. J., Fenselau, C. (2004). Investigation of doxorubicin resistance in MCF-7 breast cancer cells using shot-gun comparative proteomics with proteolytic 18O labeling. J. Proteome Res. 3, 455-462.
13. Caputo, E., Moharram, R., Martin, B. M. (2003). Methods for on-chip protein analysis. Anal. Biochem. 321, 116-124.
14. Chakraborty, A., Regnier, F. E. (2002). Global internal standard technology for comparative proteomics. J. Chromatogr. A 949, 173-184.
15. Chaurand, P., Caprioli, R. M. (2002). Direct profiling and imaging of peptides and proteins from mammalian cells and tissue sections by mass spectrometry. Electrophoresis 23, 3125-3135.
16. Chaurand, P., Schwartz, S. A., Caprioli, R. M. (2002). Imaging mass spectrometry: a new tool to investigate the spatial organization of peptides and proteins in mammalian tissue sections. Curr. Opin. Chem. Biol. 6, 676-681.
17. Chen, X., Smith, L. M., Bradbury, E. M. (2000). Site-specific mass tagging with stable isotopes in proteins for accurate and efficient protein identification. Anal. Chem. 72, 1134-1143.
18. Conrads, T. P., Alving, K., Veenstra, T. D., Belov, M. E., Anderson, G. A., Anderson, D. J., Lipton, M. S., Pasa-Tolic, L., Udseth, H. R., Chrisler, W. B., et al. (2001). Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. Anal. Chem. 73, 2132-2139.
19. Desiderio, D. M., Zhu, X. (1998). Quantitative analysis of methionine enkephalin and beta-endorphin in the pituitary by liquid secondary ion mass spectrometry and tandem mass spectrometry. J. Chromatogr. A 794, 85-96.
20. DeSouza, L., Diehl, G., Rodrigues, M. J., Guo, J., Romaschin, A. D., Colgan, T. J., Siu, K. W. (2005). Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J. Proteome Res. 4, 377-386.
21. Doroshenko, V. M., Cotter, R. J. (1995). High-performance collision-induced dissociation of peptide ions formed by matrix-assisted laser desorption/ionization in a quadrupole ion trap mass spectrometer. Anal. Chem. 67, 2180-2187.
22. Dziembowski, A., Seraphin, B. (2004). Recent developments in the analysis of protein complexes. FEBS Lett. 556, 1-6.
23. Ericson, C., Phung, Q. T., Horn, D. M., Peters, E. C., Fitchett, J. R., Ficarro, S. B., Salomon, A. R., Brill, L. M., Brock, A. (2003). An automated noncontact deposition interface for liquid chromatography matrix-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 75, 2309-2315.
24. Everley, P. A., Krijgsveld, J., Zetter, B. R., Gygi, S. P. (2004). Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol. Cell Proteomics 3, 729-735.
25. Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., Whitehouse, C. M. (1989). Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64-71.
26. Flory, M. R., Griffin, T. J., Martin, D., Aebersold, R. (2002). Advances in quantitative proteomics using stable isotope tags. Trends Biotechnol. 20, 23-29.
27. Fritze, C. E., Anderson, T. R. (2000). Epitope tagging: general method for tracking recombinant proteins. Methods Enzymol. 327, 3-16.
28. Gehrmann, M. L., Hathout, Y., Fenselau, C. (2004). Evaluation of metabolic labeling for comparative proteomics in breast cancer cells. J. Proteome Res. 3, 1063-1068.
29. Geng, M., Ji, J., Regnier, F. E. (2000). Signature-peptide approach to detecting proteins in complex mixtures. J. Chromatogr. A 870, 295-313.
30. Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., Gygi, S. P. (2003). Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 100, 6940-6945.
31. Gingras, A. C., Aebersold, R., Raught, B. (2005). Advances in protein complex analysis using mass spectrometry. J. Physiol. 563, 11-21.
32. Goshe, M. B., Smith, R. D. (2003). Stable isotope-coded proteomic mass spectrometry. Curr. Opin. Biotechnol. 14, 101-109.
33. Griffin, T. J., Han, D. K., Gygi, S. P., Rist, B., Lee, H., Aebersold, R., Parker, K. C. (2001). Toward a high-throughput approach to quantitative proteomic analysis: expression-dependent protein identification by mass spectrometry. J. Am. Soc. Mass Spectrom. 12, 1238-1246.
34. Gruhler, A., Olsen, J. V., Mohammed, S., Mortensen, P., Faergeman, N. J., Mann, M., Jensen, O. N. (2005). Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell Proteomics 4, 310-327.
35. Guo, J., Yang, E. C., Desouza, L., Diehl, G., Rodrigues, M. J., Romaschin, A. D., Colgan, T. J., Siu, K. W. (2005). A strategy for high-resolution protein identification in surface-enhanced laser desorption/ionization mass spectrometry: Calgranulin A and chaperonin 10 as protein markers for endometrial carcinoma. Proteomics 5, 1953-1966.
36. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., Aebersold, R. (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999.
37. Han, D. K., Eng, J., Zhou, H., Aebersold, R. (2001). Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946-951.
38. Haynes, P. A., Yates III, J. R., (2000). Proteome profiling-pitfalls and progress. Yeast 17, 81-87.
39. Heller, M., Mattou, H., Menzel, C., Yao, X. (2003). Trypsin catalyzed 160-to-180 exchange for comparative proteomics: tandem mass spectrometry comparison using MALDI-TOF, ESI-QTOF, and ESI-ion trap mass spectrometers. J. Am. Soc. Mass Spectrom. 14, 704-718.
40. Hoang, V. M., Conrads, T. P., Veenstra, T. D., Blonder, J., Terunuma, A., Vogel, J. C., Fisher, R. J. (2003). Quantitative proteomics employing primary amine affinity tags. J. Biomol. Tech. 14, 216-223.
41. Hochleitner, E. O., Kastner, B., Frohlich, T., Schmidt, A., Luhrmann, R., Arnold, G., Lottspeich, F. (2005). Protein stoichiometry of a multiprotein complex, the human spliceosomal U1 small nuclear ribonucleoprotein: absolute quantification using isotope-coded tags and mass spectrometry. J. Biol. Chem. 280, 2536-2542.
42. Hutchens, T. W., Yip, T. T. (1993). New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Commun. Mass Spectrom. 7, 576-580.
43. Ibarrola, N., Kalume, D. E., Gronborg, M., Iwahori, A., Pandey, A. (2003). A proteomic approach for quantification of phosphorylation using stable isotope labeling in cell culture. Anal. Chem. 75, 6043-6049.
44. Ibarrola, N., Molina, H., Iwahori, A., Pandey, A. (2004). A novel proteomic approach for specific identification of tyrosine kinase substrates using [13C]tyrosine. J. Biol. Chem. 279, 15805-15813.
45. Ippel, J. H., Pouvreau, L., Kroef, T., Gruppen, H., Versteeg, G., van den Putten, P., Struik, P. C., van Mierlo, C. P. (2004). In vivo uniform (15)N-isotope labelling of plants: using the greenhouse for structural proteomics. Proteomics 4, 226-234.
46. Jiang, H., English, A. M. (2002). Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine. J. Proteome Res. 1, 345-350.
47. Jonscher, K. R., Yates III, J. R. (1997). The quadrupole ion trap mass spectrometer - a small solution to a big challenge. Anal. Biochem. 244, 1-15.
48. Jonsson, A. P. (2001). Mass spectrometry for protein and peptide characterisation. Cell Mol. Life Sci. 58, 868-884.
49. Karas, M., Hillenkamp, F. (1988). Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60, 2299-2301.
50. Kolkman, A., Dirksen, E. H., Slijper, M., Heck, A. J. (2005). Double standards in quantitative proteomics: direct comparative assessment of difference in gel electrophoresis and metabolic stable isotope labeling. Mol. Cell Proteomics 4, 255-266.
51. Kosaka, T., Takazawa, T., Nakamura, T. (2000). Identification and C-terminal characterization of proteins from two-dimensional polyacrylamide gels by a combination of isotopic labeling and nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 72, 1179-1185.
52. Krause, E., Wenschuh, H., Jungblut, P. R. (1999). The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins. Anal. Chem. 71, 4160-4165.
53. Krijgsveld, J., Ketting, R. F., Mahmoudi, T., Johansen, J., Artal-Sanz, M., Verrijzer, C. P., Plasterk, R. H., Heck, A. J. (2003). Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat. Biotechnol. 21, 927-931.
54. Krutchinsky, A. N., Zhang, W., Chait, B. T. (2000). Rapidly switchable matrix-assisted laser desorption/ionization and electrospray quadrupole-time-of-flight mass spectrometry for protein identification. J. Am. Soc. Mass Spectrom. 11, 493-504.
55. Le Blanc, J. C., Hager, J. W., Ilisiu, A. M., Hunter, C., Zhong, F., Chu, I. (2003). Unique scanning capabilities of a new hybrid linear ion trap mass spectrometer (Q TRAP) used for high sensitivity proteomics applications. Proteomics 3, 859-869.
56. Lill, J. (2003). Proteomic tools for quantification by mass spectrometry. Mass Spectrom. Rev. 22, 182-194.
57. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., Yates III, J. R. (1999). Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17, 676-682.
58. Liu, P., Regnier, F. E. (2002). An isotope coding strategy for proteomics involving both amine and carboxyl group labeling. J. Proteome Res. 1, 443-450.
59. Loboda, A. V., Krutchinsky, A. N., Bromirski, M., Ens, W., Standing, K. G. (2000). A tandem quadrupole/time-of-flight mass spectrometer with a matrix-assisted laser desorption/ionization source: design and performance. Rapid Commun. Mass Spectrom. 14, 1047-1057.
60. MacCoss, M. J., Wu, C. C., Liu, H., Sadygov, R., Yates III, J. R. (2003). A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal. Chem. 75, 6912-6921.
61. Mann, M., Hendrickson, R. C., Pandey, A. (2001). Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70, 437-473.
62. Medzihradszky, K. F., Campbell, J. M., Baldwin, M. A., Falick, A. M., Juhasz, P., Vestal, M. L., Burlingame, A. L. (2000). The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal. Chem. 72, 552-558.
63. Meng, C. K., Mann, M., Fenn, J. B. (1988). On protons of proteins - a beams a beam for a that. Z. Phys. D 10, 361-368.
64. Mirgorodskaya, O. A., Kozmin, Y. P., Titov, M. I., Korner, R., Sonksen, C. P., Roepstorff, P. (2000). Quantification of peptides and proteins by matrix-assisted laser desorption/ionization mass spectrometry using (18)O-labeled internal standards. Rapid Commun. Mass Spectrom. 14, 1226-1232.
65. Mitulovic, G., Smoluch, M., Chervet, J. P., Steinmacher, I., Kungl, A., Mechtler, K. (2003). An improved method for tracking and reducing the void volume in nano HPLC-MS with micro trapping columns. Anal. Bioanal. Chem. 376, 946-951.
66. Mo, W., Takao, T., Shimonishi, Y. (1997). Accurate peptide sequencing by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 11, 1829-1834.
67. Molina, H., Parmigiani, G., Pandey, A. (2005). Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. Anal. Chem. 77, 2739-2744.
68. Moritz, B., Meyer, H. E. (2003). Approaches for the quantification of protein concentration ratios. Proteomics 3, 2208-2220.
69. Oda, Y., Huang, K., Cross, F. R., Cowburn, D., Chait, B. T. (1999). Accurate quantification of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. USA 96, 6591-6596.
70. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., Mann, M. (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics 1, 376-386.
71. Ong, S. E., Kratchmarova, I., Mann, M. (2003). Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC) J. Proteome Res. 2, 173-181.
72. Ong, S. E., Mittler, G., Mann, M. (2004). Identifying and quantifying in vivo methylation sites by heavy methyl SILAC. Nat. Methods 1, 119-126.
73. Opiteck, G. J., Lewis, K. C., Jorgenson, J. W., Anderegg, R. J. (1997). Comprehensive on-line LC/LC/MS of proteins. Anal. Chem. 69, 1518-1524.
74. Pasa-Tolic, L., Jensen, P. K., Anderson, G. A., Lipton, M. S., Peden, K. K., Martinovic, S., Tolic, N., Bruce, J. E., Smith, S. R. (1999). High throughput proteome-wide precision measurements of protein expression using mass spectrometry. J. Am. Chem. Soc. 121, 7949-7950.
75. Petricoin III, E. F., Ornstein, D. K., Paweletz, C. P., Ardekani, A., Hackett, P. S., Hitt, B. A., Velassco, A., Trucco, C., Wiegand, L., Wood, K., et al. (2002a). Serum proteomic patterns for detection of prostate cancer. J. Natl. Cancer Inst. 94, 1576-1578.
76. Petricoin, E. F., Ardekani, A. M., Hitt, B. A., Levine, P. J., Fusaro, V. A., Steinberg, S. M., Mills, G. B., Simone, C., Fishman, D. A., Kohn, E. C., Liotta, L. A. (2002b). Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359, 572-577.
77. Puig, O., Caspary, F., Rigaut, G., Rutz, B., Bouveret, E., Bragado-Nilsson, E., Wilm, M., Seraphin, B. (2001). The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218-229.
78. Qian, W. J., Monroe, M. E., Liu, T., Jacobs, J. M., Anderson, G. A., Shen, Y., Moore, R. J., Anderson, D. J., Zhang, R., Calvano, S. E., et al. (2005). Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach. Mol. Cell Proteomics 4, 700-709.
79. Qin, J., Herring, C. J., Zhang, X. (1998). De novo peptide sequencing in an ion trap mass spectrometer with 18O labeling. Rapid Commun. Mass Spectrom. 12, 209-216.
80. Qiu, Y., Sousa, E. A., Hewick, R. M., Wang, J. H. (2002). Acid-labile isotope-coded extractants: a class of reagents for quantitative mass spectrometric analysis of complex protein mixtures. Anal. Chem. 74, 4969-4979.
81. Ranish, J. A., Yi, E. C., Leslie, D. M., Purvine, S. O., Goodlett, D. R., Eng, J., Aebersold, R. (2003). The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 33, 349-355.
82. Ren, D., Penner, N. A., Slentz, B. E., Regnier, F. E. (2004). Histidine-rich peptide selection and quantification in targeted proteomics. J. Proteome Res. 3, 37-45.
83. Reynolds, K. J., Yao, X., Fenselau, C. (2002). Proteolytic 18O labeling for comparative proteomics: evaluation of endoprotease Glu-C as the catalytic agent. J. Proteome Res. 1, 27-33.
84. 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.
85. Riggs, L., Seeley, E. H., Regnier, F. E. (2005). Quantification of phospho-proteins with global internal standard technology. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 817, 89-96.
86. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., et al. (2004). Multiplexed protein quantification in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 3, 1154-1169.
87. Sakai, J., Kojima, S., Yanagi, K., Kanaoka, M. (2005). 18O-labeling quantitative proteomics using an ion trap mass spectrometer. Proteomics 5, 16-23.
88. Schmidt, A., Kellermann, J., Lottspeich, F. (2005). A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5, 4-15.
89. Schnolzer, M., Jedrzejewski, P., Lehmann, W. D. (1996). Proteasecatalyzed incorporation of 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry. Electrophoresis 17, 945-953.
90. Schulze, W. X., Mann, M. (2004). A novel proteomic screen for peptide-protein interactions. J. Biol. Chem. 279, 10756-10764.
91. Schwartz, J. C., Senko, M. W., Syka, J. E. (2002). A two-dimensional quadrupole ion trap mass spectrometer. J. Am. Soc. Mass Spectrom. 13, 659-669.
92. Shevchenko, A., Chernushevich, I., Ens, W., Standing, K. G., Thomson, B., Wilm, M., Mann, M. (1997). Rapid 'de novo' peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom. 11, 1015-1024.
93. Shevchenko, A., Loboda, A., Shevchenko, A., Ens, W., Standing, K. G. (2000). MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research. Anal. Chem. 72, 2132-2141.
94. Shevchenko, A., Schaft, D., Roguev, A., Pijnappel, W. W., Stewart, A. F., Shevchenko, A. (2002). Deciphering protein complexes and protein interaction networks by tandem affinity purification and mass spectrometry: analytical perspective. Mol. Cell Proteomics 1, 204-212.
95. Smith, R. D., Anderson, G. A., Lipton, M. S., Masselon, C., Pasa-Tolic, L., Shen, Y., Udseth, H. R. (2002). The use of accurate mass tags for high-throughput microbial proteomics. Omics 6, 61-90.
96. Smith, R. D., Pasa-Tolic, L., Lipton, M. S., Jensen, P. K., Anderson, G. A., Shen, Y., Conrads, T. P., Udseth, H. R., Harkewicz, R., Belov, M. E., et al. (2001). Rapid quantitative measurements of proteomes by Fourier transform ion cyclotron resonance mass spectrometry. Electrophoresis 22, 1652-1668.
97. Smolka, M., Zhou, H., Aebersold, R. (2002). Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol. Cell Proteomics 1, 19-29.
98. Smolka, M. B., Zhou, H., Purkayastha, S., Aebersold, R. (2001). Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Anal. Biochem. 297, 25-31.
99. Spengler, B. (1997). Post-source decay analysis in matrix-assisted laser desorption/ionization mass spectrometry of biomolecules. J. Mass Spectrom. 32, 1019-1036.
100. Steen, H., Mann, M. (2004). The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 5, 699-711.
101. Stewart, I. I., Thomson, T., Figeys, D. (2001). 18O labeling: a tool for proteomics. Rapid Commun. Mass Spectrom. 15, 2456-2465.
102. Stoeckli, M., Chaurand, P., Hallahan, D. E., Caprioli, R. M. (2001). Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat. Med. 7, 493-496.
103. Tang, N., Tornatore, P., Weinberger, S. R. (2004). Current developments in SELDI affinity technology. Mass Spectrom. Rev. 23, 34-44.
104. Tao, W. A., Aebersold, R. (2003). Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr. Opin. Biotechnol. 14, 110-118.
105. Terpe, K. (2003). Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems. Appl. Microbiol. Biotechnol. 60, 523-533.
106. Wang, S., Zhang, X., Regnier, F. E. (2002). Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates. J. Chromatogr. A 949, 153-162.
107. Wang, Y. K., Ma, Z., Quinn, D. F., Fu, E. W. (2001). Inverse 18O labeling mass spectrometry for the rapid identification of marker/target proteins. Anal. Chem. 73, 3742-3750.
108. Wang, Y. K., Ma, Z., Quinn, D. F., Fu, E. W. (2002). Inverse 15N-metabolic labeling/mass spectrometry for comparative proteomics and rapid identification of protein markers/targets. Rapid Commun. Mass Spectrom. 16, 1389-1397.
109. Washburn, M. P., Ulaszek, R., Deciu, C., Schieltz, D. M., Yates III, J. R. (2002). Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal. Chem. 74, 1650-1657.
110. Washburn, M. P., Ulaszek, R. R., Yates III, J. R. (2003). Reproducibility of quantitative proteomic analyses of complex biological mixtures by multidimensional protein identification technology. Anal. Chem. 75, 5054-5061.
111. Washburn, M. P., Wolters, D., Yates III, J. R. (2001). Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247.
112. Wilcox, B. E., Hendrickson, C. L., Marshall, A. G. (2002). Improved ion extraction from a linear octopole ion trap: SIMION analysis and experimental demonstration. J. Am. Soc. Mass Spectrom. 13, 1304-1312.
113. Wilm, M., Mann, M. (1996). Analytical properties of the nanoelectrospray ion source. Anal. Chem. 68, 1-8.
114. Wilm, M., Shevchenko, A., Houthaeve, T., Breit, S., Schweigerer, L., Fotsis, T., Mann, M. (1996). Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379, 466-469.
115. Wilm, M., Mann, M. (1994). Electrospray and Taylor-Cone theory, Dole's beam of macromolecules at last? Int. J. Mass Spectrom. Ion Process 136, 167-180.
116. Wolters, D. A., Washburn, M. P., Yates III, J. R. (2001). An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683-5690.
117. Yanagisawa, K., Shyr, Y., Xu, B. J., Massion, P. P., Larsen, P. H., White, B. C., Roberts, J. R., Edgerton, M., Gonzalez, A., Nadaf, S., et al. (2003). Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 362, 433-439.
118. Yao, X., Afonso, C., Fenselau, C. (2003). Dissection of proteolytic 18O labeling: endoprotease-catalyzed 16O-to-18O exchange of truncated peptide substrates. J. Proteome Res. 2, 147-152.
119. Yao, X., Freas, A., Ramirez, J., Demirev, P. A., Fenselau, C. (2001). Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal. Chem. 73, 2836-2842.
120. Yu, L. R., Conrads, T. P., Uo, T., Issaq, H. J., Morrison, R. S., Veenstra, T. D. (2004). Evaluation of the acid-cleavable isotope-coded affinity tag reagents: application to camptothecin-reated cortical neurons. J. Proteome Res. 3, 469-477.
121. Zang, L., Palmer Toy, D., Hancock, W. S., Sgroi, D. C., Karger, B. L. (2004). Proteomic analysis of ductal carcinoma of the breast using laser capture micro dissection, LC-MS, and 16O/18O isotopic labeling. J. Proteome Res. 3, 604-612.
122. Zhang, R., Regnier, F. E. (2002). Minimizing resolution of isotopically coded peptides in comparative proteomics. J. Proteome Res. 1, 139-147.
123. Zhang, R., Sioma, C. S., Wang, S., Regnier, F. E. (2001). Fractionation of isotopically labeled peptides in quantitative proteomics. Anal. Chem. 73, 5142-5149.
124. Zhou, H., Boyle, R., Aebersold, R. (2004). Quantitative protein analysis by solid phase isotope tagging and mass spectrometry. Methods Mol. Biol. 261, 511-518.
125. Zhou, H., Ranish, J. A., Watts, J. D., Aebersold, R. (2002). Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat. Biotechnol. 20, 512-515.