Achieving in-depth proteomics profiling by mass spectrometry

ACS Chemical Biology

Volumn 2, Issue 1, 2007, Pages 39-52

  Ahn, Natalie G ^a   Shabb, John B ^b   Old, William M ^a   Resing, Katheryn A ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF NORTH DAKOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PROTEIN; PROTEOME;

AMINO ACID SEQUENCE; ANALYTIC METHOD; COLLISIONALLY ACTIVATED DISSOCIATION; ELECTRON CAPTURE DETECTION; ELECTROSPRAY MASS SPECTROMETRY; HUMAN; INFRARED SPECTROSCOPY; ION MOBILITY SPECTROMETRY; ION TRAP MASS SPECTROMETRY; ISOTOPE LABELING; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN LOCALIZATION; PROTEIN METABOLISM; PROTEOMICS; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; REVIEW; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TRANSLATION INITIATION; TWO DIMENSIONAL GEL ELECTROPHORESIS; ANIMAL; METHODOLOGY; PROTEIN MICROARRAY;

ANIMALS; HUMANS; MASS SPECTROMETRY; PROTEIN ARRAY ANALYSIS; PROTEOME; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 33947541574     PISSN: 15548929     EISSN: None     Source Type: Journal    
DOI: 10.1021/cb600357d     Document Type: Review

References (113)

1. Celis, J. E., Gromov, P., Ostergaard, M., Madsen, P., Honore, B, Dejgaard, K., Olsen, E., Vorum, H., Kristensen, D. B., Gromova, I., Haunso, A., Van Damme, J., Puype, M., Vandekerckhove, J., and Rasmussen, H. H. (1996) Human 2-D PAGE databases for proteome analysis in health and disease: http://biobase.dk/cgi-bin/celis, FEBS Lett. 398, 129-134.
2. Domon, B., and Aebersold, R. (2006) Mass spectrometry and protein analysis, Science 312, 212-217.
3. Henzel, W. J., Watanabe, C., and Stults, J. T. (2003) Protein identification: the origins of peptide mass fingerprinting, J. Am. Soc. Mass Spectrom. 14, 931-942.
4. Morts, E., O'Connor, P. B., Roepstorff, P., Kelleher, N. L., Wood, T. D., McLafferty, F. W., and Mann, M. (1996) Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases, Proc. Natl. Acad. Sci. U.S.A. 93, 8264-8267.
5. Zhang, W., and Chait, B. T. (2000) ProFound: an expert system for protein identification using mass spectrometric peptide mapping information, Anal. Chem. 72, 2482-2489.
6. Pappin, D. J. C., Hojrup, P., and Bleasby, A. J. (1993) Rapid identification of proteins by peptide mass fingerprinting, Curr. Biol. 3, 327-332.
7. Covey, T. R., Banner, R. F., Shushan, B. I., and Henion, J. (1988) The determination of protein, oligonucleotide and peptide molecular weights by ion-spray mass spectrometry, Rapid Comm. Mass Spectrom. 2, 249-256.
8. Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels, Anal. Chem. 68, 850-858.
9. Hillenkamp, F., Karas, M., Beavis, R. C., and Chait, B. T. (1991) Matrix-assisted laser desorption ionization of biopolymers, Anal. Chem. 63, 1193A-1203A.
10. Celis, J. E., and Gromov, P. (2003) Proteomics in translational cancer research: toward an integrated approach, Cancer Cell 3, 9-15.
11. Chen, G., Gharib, T. G., Wang, H., Huang, C. C., Kuick, R., Thomas, D. G., Shedden, K. A., Misek, D. E., Taylor, J. M., Giordano, T. J., Kardia, S. L., Iannettoni, M. D., Yee, J., Hogg, P. J., Orringer, M. B., Hanash, S. M., and Beer, D. G. (2003) Protein profiles associated with survival in lung adenocarcinoma, Proc. Natl. Acad. Sci. U.S.A. 100, 13537-13542.
12. Lewis, T. S., Hunt, J. B., Aveline, L. D., Jonscher, K. R., Louie, D. F., Yeh, J. M., Nahreini, T. S., Resing, K. A., and Ahn, N. G. (2000) Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry, Mol. Cell 6, 1343-1354.
13. Kanamoto, T., Hellman, U., Heldin, C. H., and Souchelnytskyi, S. (2002) Functional proteomics of transforming growth factor-beta1-stimulated MV1Lu epithelial cells: Rad51 as a target of TGF-beta1-dependent regulation of DNA repair, EMBO J. 21, 1219-1230.
14. Zuo, X., and Speicher, D. W. (2002) Comprehensive analysis of complex proteomes using microscale solution isoelectrofocusing prior to narrow pH range two-dimensional electrophoresis, Proteomics 2, 58-68.
15. Klose, J., Nock, C., Herrmann, M., Stuhler, K., Marcus, K., Bluggel, M., Krause, E, Schalkwyk, L. C., Rastan, S., Brown, S. D., Bussow, K., Himmelbauer, H., and Lehrach, H. (2002) Genetic analysis of the mouse brain proteome, Nat. Genet. 30, 385-393.
16. Hunt, D. F., Henderson, R. A., Shabanowitz, J., Sakaguchi, K., Michel, H., Sevilir, N., Cox, A.L., Appella, E., and Engelhard, V. H. (1992) Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry, Science 255, 1261-1263.
17. Davis, M. T., Stahl, D. C., Hefta, S. A., and Lee, T. D. (1995) A microscale electrospray interface for on-line, capillary liquid chromatography/tandem mass spectrometry of complex peptide mixtures, Anal. Chem. 67, 4549-4556.
18. Courchesne, P. L., Jones, M. D., Robinson, J. H., Spahr, C. S., Mc-Cracken, S., Bentley, D. L., Luethy, R., and Patterson, S. D. (1998) Optimization of capillary chromatography ion trap-mass spectrometry for identification of gel-separated proteins, Electrophoresis 19, 956-967.
19. Figeys, D., and Aebersold, R. (1997) High Sensitivity identification of proteins by electrospray ionization tandem mass spectrometry: initial comparison between an ion trap mass spectrometer and a triple quadrupole mass spectrometer, Electrophoresis 18, 360-368.
20. Anderegg, R. J., Wagner, D. S., Blackburn, R. K., Opiteck, G. J., and Jorgenson, J. W. (1997) A multidimensional approach to protein characterization, J. Protein Chem. 16, 523-526.
21. Opiteck, G. J., Lewis, K. C., Jorgenson, J. W., and Anderegg, R. J. (1997) Comprehensive on-line LC/LC/MS of proteins, Anal. Chem. 69, 1518-1524.
22. Figeys, D., Gygi, S. P., Zhang, Y., Watts, J., Gu, M., and Aebersold, R. (1998) Electrophoresis combined with novel mass spectrometry techniques: powerful tools for the analysis of proteins and proteomes, Electrophoresis 19, 1811-1818.
23. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., and Yates, J. R. (1999) Direct analysis of protein complexes using mass spectrometry, Nat. Biotechnol. 17, 676-682.
24. Washburn, M. P., Wolters, D., and Yates, J. R. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology, Nat. Biotechnol. 19, 242-247.
25. Spahr, C. S., Davis, M. T., McGinley, M. D., Robinson, J. H., Bures, E. J., Beierle, J., Mort, J., Courchesne, P. L., Chen, K., Wahl, R. C., Yu, W., Luethy, R., and Patterson, S. D. (2001) Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest, Proteomics 1, 93-107.
26. Engwegen, J., Gast, M., Schellens, J., and Beijnen, J. (2006) Clinical proteomics: searching for better tumor markers with SELDI-TOF mass spectrometry, Trends Pharmacol. Sci. 27, 251-259.
27. Louie, D. F., Resing, K. A., Lewis, T. S., and Ahn, N. G. (1996) Mass spectrometric analysis of 40 S ribosomal proteins from Rat-1 fibroblasts, J. Biol. Chem. 271, 28189-28198.
28. Krishnamurthy, T., Davis, M. T., Stahl, D. C., and Lee, T. D. (1999) liquid chromatography/microspray mass spectrometry for bacterial investigations, Rapid Commun. Mass Spectrom. 13, 39-49.
29. Cooper, H. J., Hakansson, K., and Marshall, A. G. (2005) The role of electron capture dissociation in biomolecular analysis, Mass Spectrom. Rev. 24, 201-222.
30. Lee, S. W., Berger, S. J., Martinovic, S., Pasa-Tolic, L, Anderson, G. A., Shen, Y., Zhao, R., and Smith, R. D. (2002) Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR, Proc. Natl. Acad. Sci. U.S.A. 99, 5942-5947.
31. Macek, B., Waanders, L. F., Olsen, J. V., and Mann, M. (2006) Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer, Mol. Cell. Proteomics 5, 949-958.
32. Patrie, S. M., Ferguson, J. T., Robinson, D. E., Whipple, D., Rother, M., Metcalf, W. W., and Kelleher, N. L. (2006) Top down mass spectrometry of <60-kDa proteins from Methanosarcina acetivorans using quadrupole FRMS with automated octopole collisionally activated dissociation, Mol. Cell. Proteomics 5, 14-25.
33. Beck, H. C., Nielsen, E. C., Matthiesen, R., Jensen, L. H., Sehested, M., Finn, P., Grauslund, M., Hansen, A. M., and Jensen, O. N. (2006) Quantitative proteomic analysis of post-translational modifications of human histones, Mol. Cell. Proteomics 5, 1314-1325.
34. Hastie, N. D., and Bishop, J. O. (1976) The expression of three abundance classes of messenger RNA in mouse tissues, Cell 9, 761-774.
35. Jongeneel, C. V., Iseli, C., Stevenson, B. J., Riggins, G. J., Lal, A., Mackay, A., Harris, R. A., O'Hare, M. J., Neville, A. M., Simpson, A. J., and Strausberg, R. L. (2003) Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing, Proc. Natl. Acad. Sci. U.S.A. 100, 4702-4705.
36. Everley, P. A., Krijgsveld, J., Zetter, B. R., and 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.
37. Kislinger, T., Cox, B., Kannan, A., Chung, C., Hu, P., Ignatchenko, A., Scott, M. S., Gramolini, A. O., Morris, Q., Hallett, M. T., Rossant, J., Hughes, T. R., Frey, B., and Emili, A. (2006) Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling, Cell 125, 173-186.
38. Patwardhan, A. J., Strittmatter, E. F., Camp, D. G., Smith, R. D., and Pallavicini, M. G. (2005) Comparison of normal and breast cancer cell lines using proteome, genome, and interactome data, J. Proteome Res. 4, 1952-1960.
39. Tian, Q., Stepaniants, S. B., Mao, M., Weng, L., Feetham, M. C., Doyle, M. J., Yi, E. C., Dai, H., Thorsson, V., Eng, J., Goodlett, D., Berger, J. P., Gunter, B., Linseley, P. S., Stoughton, R. B., Aebersold, R., Collins, S. J., Hanlon, W. A., and Hood, L. E. (2004) Integrated genomic and proteomic analyses of gene expression in mammalian cells, Mol. Cell. Proteomics. 3, 960-969.
40. Resing, K. A., Meyer-Arendt, K., Mendoza, A. M., Aveline-Wolf, L. D., Jonscher, J. R., Pierce, K. G., Old, W. M., Cheung, H. T., Russell, S., Wattawa, J. L., Goehle, G. R., Knight, R. D., and Ahn, N. G. (2004) Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics, Anal. Chem. 76, 3556-3568.
41. Shen, Y., Zhao, R., Belov, M. E., Conrads, T. P., Anderson, G. A., Tang, K., Pasa-Tolic, L., Veenstra, T. D., Lipton, M. S., Udseth, H. R., and Smith, R. D. (2001) Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics, Anal. Chem. 73, 1766-1775.
42. Liu, X., Plasencia, M., Ragg, S., Valentine, S. J., and Clemmer, D. E. (2004) Development of high throughput dispersive LC-ion mobility-TOFMS techniques for analysing the human plasma proteome, Brief Funct. Genomic Proteomic 3, 177-86.
43. Koeniger, S. L, Merenbloom, S. I., Valentine, S. J., Jarrold, M. F., Udseth, H. R., Smith, R. D., and Clemmer, D. E. (2006) An IMS-IMS analogue of MS-MS, Anal. Chem. 78, 4161-4174.
44. Sadygov, R. G., Cociorva, D., and Yates, J. R. (2004) Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat. Methods 1, 195-202.
45. Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data, Mol. Cell. Proteomics 4, 1419-1440.
46. Johnson, R. S., Davis, M. T., Taylor, J. A., and Patterson, S. D. (2005) Informatics for protein identification by mass spectrometry, Methods 35, 223-236.
47. Russell S. A., Old, W., Resing, K. A., and Hunter, L. (2006) Proteomic informatics, Int. Rev. Neurobiol. 61, 127-157.
48. Kapp, E. A., Schutz, F., Connolly, L. M., Chakel, J. A., Meza, J. E., Miller, C. A., Fenyo, D., Eng, J. K., Adkins, J. N., Omenn, G. S., and Simpson, R. J. (2005) An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis, Proteomics 5, 3475-3490.
49. Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M., Maynard, D. M., Yang, X., Shi, W., and Bryant, S. H. (2004) Open mass spectrometry search algorithm, J. Proteome Res. 3, 958-964.
50. Keller, A., Nesvizhskii, A. I., Kolker, E., and 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.
51. Eng, J. K., McCormack, A. L., and Yates, J. R. (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.
52. Petritis, K., Kangas, L. J., Yan, B., Monroe, M. E., Strittmatter, E. F., Qian, W. J., Adkins, J. N., Moore, R. J., Xu, Y., Lipton, M. S., Camp, D. G., and Smith, R. D. (2006) Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information, Anal. Chem. 78, 5026-5039.
53. Huang, Y., Triscari, J. M., Tseng, G. C., Pasa-Tolic, L., Lipton, M. S., Smith, R. D., and Wysocki, V. H. (2005) Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns, Anal. Chem. 77, 5800-5813.
54. Gibbons, F. D., Elias, J. E., Gygi, S. P., and Roth, F. P. (2004) SILVER helps assign peptides to tandem mass spectra using intensity-based scoring, J. Am. Soc. Mass Spectrom. 15, 910-912.
55. Craig, R., Cortens, J. P., and Beavis, R. C. (2005) The use of proteotypic peptide libraries for protein identification, Rapid Commun. Mass Spectrom. 19, 1844-1850.
56. Frewen, B. E., Merrihew, G. E., Wu, C. C., Noble, W. S., and MacCoss, M. J. (2006) Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem. 78, 5678-5684.
57. Wysocki, V. H., Resing, K. A., Zhang, Q., and Cheng, G. (2004) Mass spectrometry of peptides and proteins, Methods 35, 211-222.
58. Wysocki, V. H., Tsaprailis, G., Smith, L. L., and Breci, L. A. (2000) Mobile and localized protons: a framework for understanding peptide dissociation, J. Mass Spectrom. 35, 1399-1406.
59. Paizs, B., and Suhai, S. (2005) Fragmentation pathways of protonated peptides, Mass Spectrom. Rev. 24, 508-548.
60. Zhang, Z. (2004) Prediction of low-energy collision-induced dissociation spectra of peptides, Anal. Chem. 76, 3908-3922.
61. Zhang, Z. (2005) Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges, Anal. Chem. 77, 6364-6373.
62. Sun, S., Meyer-Arendt, K., Eichelberger, B., Brown, R., Yen, C. Y., Old, W.M., Pierce, K., Cios, K., Ahn, N. G., and Resing, K. A. (2007) Improved validation of peptide MS/MS assignments using spectral intensity prediction, Mol. Cell. Proteomics, 6, 1-17
63. Tabb, D. L., McDonald, W. H., and Yates, J. R. (2002) DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics, J. Proteome Res. 1, 21-26.
64. Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry, Anal. Chem. 75, 4646-4658.
65. Yang, X., Dondeti, V., Dezube, R., Maynard, D. M., Geer, L. Y., Epstein, J., Chen, X., Markey, S. P., and Kowalak, J. A. (2004) DBParser: web-based software for shotgun proteomic data analyses, J. Proteome Res. 3, 1002-1008.
66. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags, Nat. Biotechnol. 17, 994-999.
67. Brown, K. J., and Fenselau, C. (2004) Investigation of doxorubicin resistance in MCF-7 breast cancer cells using shotgun proteomics with proteolytic 180 labeling, J. Proteome Res. 3, 455-462.
68. Cagney, G., and Emili, A. (2002) De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging, Nat. Biotechnol. 20, 163-170.
69. Berger, S. J., Lee, S. W., Anderson, G. A., Pasa-Tolic, L, Tolic, N., Shen, Y., Zhao, R., and Smith, R. D. (2002) High-throughput global peptide proteomic analysis by combining stable isotope amino acid labeling and data-dependent multiplexed-MS/MS. Anal. Chem. 74, 4994-5000.
70. Ong, S. E, Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., and 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. 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., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., and Pappin, D. J. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents, Mol. Cell. Proteomics 3, 1154-1169.
72. Parker, K. C., Patterson, D., Williamson, B., Marchese, J., Graber, A., He, F., Jacobson, A., Juhasz, P., and Martin, S. (2004) Depth of proteome issues: a yeast isotope-coded affinity tag reagent study, Mol. Cell. Proteomics 3, 625-659.
73. Beynon, R. J., and Pratt, J. M. (2005) Metabolic labeling of proteins for proteomics, Mol. Cell. Proteomics 4, 857-872.
74. Bondarenko, P. V., Chelius, D., and Shaler, T. A. (2002) Identification and relative quantification of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry, Anal. Chem. 74, 4741-4749.
75. Wang, W., Zhou, H., Lin, H., Roy, S., Shaler, T., Hill, L, Norton, S., Kumar, P, Anderle, M., and Becker, C. (2003) Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards, Anal. Chem. 75, 4818-4826.
76. Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G., Mendoza, A., Sevinsky, J. R., Resing, K. A., and Ahn, N. G. (2005) Comparison of label free methods for quantifying human proteins by shotgun proteomics, Mol. Cell. Proteomics 4, 1487-1502.
77. Wang, G., Wu, W. W., Zeng, W., Chou, C. L., and Shen, R. F. (2006) Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: reproducibility, linearity, and application with complex proteomes, J. Proteome Res. 5, 1214-1223.
78. Fang, R., Elias, D. A., Monroe, M. E., Shen, Y., Mcintosh, M., Wang, P., Goddard, C. D., Callister, S. J., Moore, R. J., Gorby, Y. A., Adkins, J. N., Fredrickson, J. K., Lipton, M. S., and Smith, R. D. (2006) Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach, Mol. Cell. Proteomics 5, 714-725.
79. Wiener, M. C., Sachs, J. R., Deyanova, E. G., and Yates, N. A. (2004) Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures, Anal. Chem. 76, 6085-6096.
80. Bonneil, E., Tessier, S., Carrier, A., and Thibault, P. (2005) Multiplex multidimensional nanoLC-MS system for targeted proteomic analyses, Electrophoresis 26, 4575-4589.
81. Conrads, T. P., Anderson, G. A., Veenstra, T. D., Pasa-Tolic, L., and Smith, R. D. (2000) Utility of accurate mass tags for proteome-wide protein identification, Anal. Chem. 72, 3349-3354.
82. Ono, M., Shitashige, M., Honda, K., Isobe, T., Kuwabara, H., Matsuzuki, H., Hirohashi, S., and Yamada, T. (2006) Label-free quantitative proteomics using large peptide data sets generated by nano-flow liquid chromatography and mass spectrometry, Mol. Cell. Proteomics 5, 1338-1347.
83. Bellew, M., Coram, M., Fitzgibbon, M., Igra, M., Randolph, T., Wang, P., May, D., Eng, J., Fang, R., Lin, C., Chen, J., Goodlett. D., Whiteaker, J., Paulovich, A., and McIntosh, M. (2006) A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS, Bioinformatics 22, 1902-1909.
84. Jaffe, J. D., Mani, D. R., Leptos, K. C., Church, G. M., Gillette, M. A., and Carr, S. A. (2006) PEPPeR: a platform for experimental proteomic pattern recognition, Mol. Cell. Proteomics 5, 1927-1941.
85. Liu, H., Sadygov, R. G., and Yates, J. R. (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics, Anal. Chem. 76, 4193-4201.
86. Zybailov, B., Coleman, M. K., Florens, L., and Washburn, M. P. (2005) Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling, Anal. Chem. 77, 6218-6224.
87. Covey, T., Maylin, G., and Henion, J. (1985) Quantitative secondary ion monitoring gas chromatography/mass spectrometry of diethylstilbestrol in bovine liver, Biomed. Mass Spectrom. 12, 274-287.
88. Lin, S., Shaler, T. A., and Becker, C. H. (2006) Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap, Anal. Chem. 78, 5762-5767.
89. Anderson, L., and Hunter, C. L. (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins, Mol. Cell. Proteomics 5, 573-588.
90. Zahedi, R. P., Sickmann, A., Boehm, A. M., Winkler, C., Zufall, N., Schönfisch, B., Guiard, B., Pfanner, N., and Meisinger, C. (2006) Proteomic analysis of the yeast mitochondrial outer membrane reveals accumulation of a subclass of preproteins, Mol. Biol. Cell 17, 1436-1450.
91. Dunkley, T. P. J., Hester, S., Shadforth, I. P., Runions, J., Weimar, T., Hanton, S. L., Griffin, J. L., Bessant, C., Brandizzi, F., Hawes, C., Watson, R. B., Dupree, P., and Lilley, K. S. (2006) Mapping the Arabidopsis organelle proteome, Proc. Natl. Acad. Sci. U.S.A. 103, 6518-6523.
92. Foster, L. J., de Hoog, C. L., Zhang, Y., Zhang, Y., Xie, X., Mootha, V. K., and Mann, M. (2006) A mammalian organelle map by protein correlation profiling, Cell 125, 187-199.
93. Andersen, J. S., Lyon, C. E., Fox, A. H., Leung, A. K., Lam, Y. W., Steen, H., Mann, M., and Lamond, A. I. (2002) Directed proteomic analysis of the human nucleolus, Curr. Biol. 12, 1-11.
94. Andersen, J. S., Lam, Y. W., Leung, A. K., Ong, S. E., Lyon, C. E., Lamond, A. I., and Mann, M. (2005) Nucleolar proteome dynamics, Nature 433, 77-83.
95. Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., and O'Shea, E. K. (2003) Global analysis of protein localization in budding yeast, Nature 425, 686-691.
96. Beausoliel, S. A., Jedrychowski, M., Schwartz, D., Elias, J. E., Villén, J., Li, J., Cohn, M. A., Cantley, L. C., and Gygi, S. P. (2004) large-scale characterization of HeLa cell nuclear phosphoproteins, Proc. Natl. Acad. Sci. U.S.A. 101, 12130-12135.
97. 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. (2005) Immunoaffinity profiling of tyrosine phosphorylation in cancer cells, Nat. Biotechnol. 23, 94-101.
98. Nousiainen, M., Silljé, H. W., Sauer, G., Nigg, E. A., and Kömer, R. (2006) Phosphoproteome analysis of the human mitotic spindle, Proc. Natl. Acad. Sci. U.S.A. 103, 5391-5396.
99. Moser, K., and White, F. M. (2006) Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-MS/MS, J. Proteome Res. 5, 98-104.
100. Gruhler, A., Olsen, J. V., Shabaz, M., Mortensen, P., Færgemann, N. J., Mann, M., and Jensen, O. N. (2005) Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway, Mol. Cell. Proteomics 4, 310-327.
101. Pandey, A., Podtelejnikov, A. V., Blagoev, B., Bustelo, X. R., and Mann, M. (2000) Analysis of receptor signaling pathways by mass spectrometry: identification of Vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors, Proc. Natl. Acad. Sci. U.S.A. 97, 179-184.
102. Larsen, M. R., Thingholm, T. E., Jensen, O. N., Poepstorff, P., and Jørgensen, J. D. (2005) highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns, Mol. Cell. Proteomics 4, 873-886.
103. Tholey, A., Reed, J., and Lehmann, W. D. (1999) Electrospray tandem mass spectrometric studies of phosphopeptides and phosphopeptide analogues, J. Mass Spectrom. 34, 117-123.
104. Syka, J. E., Coon, J. J., Schroeder, M. J., Shabanowitz, J., and Hunt, D. F. (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry, Proc. Natl. Acad. Sci. U.S.A. 101, 9528-9533.
105. McLachlin, D. T., and Chait, B. T. (2003) Improved beta-elimination-based affinity purification strategy for enrichment of phosphopeptides, Anal. Chem. 75, 6826-6836.
106. Tseng, H.C., Ovaa, H., Wei, N.J., Ploegh, H., and Tsai, L. H. (2005) Phosphoproteomic analysis with a solid-phase capture-release-tag approach, Chem. Biol. 12, 769-777.
107. Tao, W. A., Wollscheid, B., O'Brien, R., Eng, J. K., Li, X. J., Bodenmiller, B., Watts, J. D., Hood, L., and Aebersold, R. (2005) Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry, Nat. Methods 2, 591-598.
108. Blagoev, B., Ong, S.-E., Kratchmarova, I., and Mann, M. (2004) Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics, Nat. Biotechnol. 22, 1139-1145.
109. Zheng, H., Hu, P., Quinn, D. F., and Wang, Y. K. (2005) Phosphotyrosine proteomic study of interferon α signaling pathway using a combination of immunoprecipitation and immobilized metal affinity chromatography, Mol. Cell. Proteomics 4, 721-730.
110. Zhang, Y., Wolf-Yadlin, A., Ross, P. L., Pappin, D. J., Rush, J., Lauffenburger, D. A., and White, F. M. (2005) time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules, Mol. Cell. Proteomics 4, 1240-1250.
111. Cantin, G. T., Venable, I. D., Cociorva, D., and Yates, J. R. (2006) Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway. J. Proteome Res. 5, 127-134.
112. Carr, S. A., Annan, R. S., and Huddleston, M. J. (2005) Mapping posttranslational modifications of proteins by MS-based selective detection: application to phosphoproteomics, Methods Enzymol. 405, 82-115.
113. Williamson, B. L., Marchese, J., and Morrice, N. A. (2006) Automated identification and quantification of protein phosphorylation sites by LC/ MS on a hybrid triple quadrupole linear ion trap mass spectrometer, Mol. Cell. Proteomics 5, 337-346.