Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics

Molecular and Cellular Proteomics

Volumn 5, Issue 12, 2006, Pages 2384-2391

  Nielsen, Michael L ^a   Savitski, Mikhail M ^a   Zubarev, Roman A ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PEPTIDE; PROTEOME;

ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; HUMAN; HUMAN CELL; IN VITRO STUDY; IN VIVO STUDY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEOMICS; SAMPLE; TANDEM MASS SPECTROMETRY;

AMINO ACID SEQUENCE; AUTOMATIC DATA PROCESSING; HUMANS; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; TUMOR CELLS, CULTURED;

EID: 33846010726     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M600248-MCP200     Document Type: Article

References (50)

1. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431, 931-945
2. Brett, D., Pospisil, H., Valcarcel, J., Reich, J., and Bork, P. (2002) Alternative splicing and genome complexity. Nat. Genet. 30, 29 -30
3. Modrek, B., and Lee, C. (2002) A genomic view of alternative splicing. Nat. Genet. 30, 13-19
4. Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G., Tammana, H., and Gingeras, T. R. (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14, 331-342
5. Creasy, D. M., and Cottrell, J. S. (2004) Unimod: protein modifications for mass spectrometry. Proteomics 4, 1534-1536
6. Meri, S., and Baumann, M. (2001) Proteomics: posttranslational modifications, immune responses and current analytical tools. Biomol. Eng. 18, 213-220
7. Wolters, D. A., Washburn, M. P., and Yates, J. R. (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683-5690
8. Anderson, N. L., and Anderson, N. G. (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol Cell. Proteomics 1, 845-867
9. Anderson, N. L., Polanski, M., Pieper, R., Gatlin, T., Tirumalai, R. S., Conrads, T. P., Veenstra, T. D., Adkins, J. N., Pounds, J. G., Fagan, R., and Lobley, A (2004) The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol. Cell. Proteomics 3, 311-326
10. De Godoy, L. M., Olsen, J. V., De Souza, G. A., Li, G., Mortensen, P., and Mann, M. (2006) Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol 7, R50
11. Wilm, M., Shevchenko, A., Houthaeve, T., Breit, S., Schweigerer, L., Fotsis, T., and Mann, M. (1996) Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379, 466-469
12. Chao, C. C., Ma, Y. S., and Stadtman, E. R. (1997) Modification of protein surface hydrophobicity and methionine oxidation by oxidative systems. Proc. Natl. Acad. Sci. U. S. A. 94, 2969-2974
13. Levine, R. L., Mosoni, L., Berlett, B. S., and Stadtman, E. R. (1996) Methionine residues as endogenous antioxidants in proteins. Proc. Natl. Acad. Sci. U. S. A 93, 15036-15040
14. Chelius, D., Rehder, D. S., and Bondarenko, P. V. (2005) Identification and characterization of deamidation sites in the conserved regions of human Immunoglobulin Gamma antibodies. Anal. Chem. 77, 6004-6011
15. Huang, L. H., Li, J. R., Wroblewski, V. J., Beals, J. M., and Riggin, R. M.. (2005) In vivo deamidation characterization of monoclonal antibody by LC/MS/MS. Anal. Chem. 77, 1432-1439
16. Karty, J. A., and Reilly, J. P. (2005) Deamidation as a consequence of beta-elimination of phosphopeptides. Anal. Chem. 77, 4673-4676
17. Robinson, A., and Robinson, L. (1991) Distribution of glutamine and asparagine residues and their near neighbors in peptides and proteins. Proc. Natl. Acad. Sci. U. S. A. 88, 8880-8884
18. Wilmarth, P. A., Tanner, S., Dasari, S., Nagalla, S. R., Riviere, M. A., Bafna, V., Pevzner, P. A., and David, L. L. (2006) Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility. J. Proteome Res. 5, 2554-2566
19. 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
20. Jones, R. C., Thyparambil, S., Taylor, J. T., and Edmondson, R. D. (2006) False discovery rates in protein identification, in 54th American Society for Mass Spectrometry Conference on Mass Spectrometry, Seattle, May 27-June 1, 2006, American Society for Mass Spectrometry, Santa Fe, NM
21. 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
22. Nielsen, M. L., Savitski, M. M., and Zubarev, R. A. (2005) Improving protein identification using complementary fragmentation techniques in Fourier transform mass spectrometry. Mol. Cell. Proteomics 4, 835-845
23. Chalkley, R. J., Baker, P. R., Hansen, K. C., Medzihradszky, K. F., Allen, N. P., Rexach, M., and Burlingame, A. L. (2005) Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by search engines. Mol. Cell. Proteomics 4, 1189-1193
24. Savitski, M. M., Nielsen, M. L., and Zubarev, R. A. (2005) New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques. Mol Cell. Proteomics 4, 1180-1188
25. Savitski, M. M., Nielsen, M. L., Kjeldsen, F., and Zubarev, R. A. (2005) Proteomics-grade de novo sequencing approach. J. Proteome Res. 4, 2348-2354
26. Savitski, M. M., Nielsen, M. L., and Zubarev, R. A. (2006) ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures. Mol. Cell. Proteomics 5, 935-948
27. Zubarev, R. A., Kelleher, N. L., and McLafferty, F. W. (1998) Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc. 120, 3265-3266
28. Savitski, M. M., Kjeldsen, F., Nielsen, M. L., and Zubarev, R. (2006) Complementary sequence preferences of electron-capture dissociation and vibrational excitation in fragmentation of polypeptide polycations. Angew. Chem. Int. Ed. Engl. 45, 5301-5303
29. Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence data-bases using mass spectrometry data. Electrophoresis 20, 3551-3567
30. Olsen, J. V., Ong, S. E., and Mann, M. (2004) Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell. Proteomics 3, 608-614
31. Stadtman, E. R. (1992) Protein oxidation and aging. Science 257, 1220-1224
32. Ambler, R. P., and Rees, M. W. (1959) Epsilon-N-Methyl-lysine in bacterial flagellar protein. Nature 184, 56-57
33. Goodleft, D. R., Armstrong, F. B., Creech, R. J., and van Breemen, R. B. (1990) Formylated peptides from cyanogen bromide digests identified by fast atom bombardment mass spectrometry. Anal. Biochem. 186, 116-120
34. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685
35. Previero, A., Coletti-Previero, M. A., and Jolles, P. (1967) Localization of non-essential tryptophan residues for the biological activity of lysozyme. J. Mol. Biol. 24, 261-268
36. Potgieter, H. C., Ubbink, J. B., Bissbort, S., Bester, M. J., Spies, J. H., and Vermaak, W. J. (1997) Spontaneous oxidation of methionine: effect on the quantification of plasma methionine levels. Anal. Biochem. 248, 86-93
37. Taylor, S. W., Fahy, E., Murray, J., Capaldi, R. A., and Ghosh, S. S. (2003) Oxidative post-translational modification of tryptophan residues in cardiac mitochondrial proteins. J. Biol. Chem. 278, 19587-19590
38. Janmey, P. A., Hvidt, S., Oster, G. F., Lamb, J., Stossel, T. P., and Hartwig, J. H. (1990) Effect of ATP on actin filament stiffness. Nature 347, 95-99
39. Pollard, T. D., and Cooper, J. A. (1986) Actin and actin-binding proteins. A critical evaluation of mechanisms and functions. Annu. Rev. Biochem. 55, 987-1035
40. Adams, C. M., and Zubarev, R. A. (2005) Distinguishing and quantifying peptides and proteins containing D-amino acids by tandem mass spectrometry. Anal. Chem. 77, 4571-4580
41. Nielsen, M. L., Savitski, M. M., Kjeldsen, F., and Zubarev, R. A. (2004) Physicochemical properties determining the detection probability of tryptic peptides in Fourier transform mass spectrometry. A correlation study. Anal. Chem. 76, 5872-5877
42. Bewick, V., Cheek, L., and Ball, J. (2003) Statistics review 7: correlation and regression. Crit. Care 7, 451-459
43. Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature 425, 737-741
44. Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., and Gygi, S. P. (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
45. Shevchenko, A., Sunyaev, S., Loboda, A., Bork, P., Ens, W., and Standing, K. G. (2001) Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Anal. Chem. 73, 1917-1926
46. Lee, H. K., Picotti, P., Domon, B., and Aebersold, R. (2006) Novel approach to identify low abundance biomarkers in serum, in 54th American Society for Mass Spectrometry Conference on Mass Spectrometry, Seattle, May 27-June 1, 2006, American Society for Mass Spectrometry, Santa Fe, NM
47. Tsur, D., Tanner, S., Zandi, E., Bafna, V., and Pevzner, P. A. (2005) Identification of post-translational modifications by blind search of mass spectra. Nat. Biotechnol. 23, 1562-1567
48. Zubarev, R. A. (2006) Protein primary structure using orthogonal fragmentation techniques in Fourier transform mass spectrometry. Expert Rev. Proteomics 3, 251-261
49. O'Farrell, P. H. (1975) High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007-4021
50. Schulze, W. X., and Mann, M. (2004) A novel proteomic screen for peptide-protein interactions. J. Biol. Chem. 279, 10756-10764