Improving protein identification using complementary fragmentation techniques in fourier transform mass spectrometry

Molecular and Cellular Proteomics

Volumn 4, Issue 6, 2005, Pages 835-845

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

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; CONTROLLED STUDY; ELECTRON CAPTURE DETECTION; ESCHERICHIA COLI; FOURIER TRANSFORM MASS SPECTROMETRY; LIQUID CHROMATOGRAPHY; MOLECULAR WEIGHT; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SCORING SYSTEM; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE;

CYCLOTRONS; ELECTRONS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MASS SPECTROMETRY; NANOTECHNOLOGY; PEPTIDES; PROTEINS; PROTEOMICS; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

ESCHERICHIA COLI;

EID: 21044441542     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.T400022-MCP200     Document Type: Article

References (41)

1. Pandey, A., and Mann, M. (2000) Proteomics to study genes and genomes. Nature 405, 837-846
2. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
3. Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C., Grimley, C., and Watanabe, C. (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. U. S. A. 90, 5011-5015
4. Zubarev, R. A., Demirev, P. A., Hakansson, P., and Sundqvist, B. U. (1995) Approaches and limits for accurate mass characterization of large biomolecules. Anal. Chem. 67, 3793-3798
5. Cargile, B. J., and Stephenson, J. L., Jr. (2004) An alternative to tandem mass spectrometry: isoelectric point and accurate mass for the identification of peptides. Anal. Chem. 76, 267-275
6. Hunt, D. F., Yates, J. R., Shabanowitz, J., Winston, S., and Hauer, C. R. (1986) Protein sequencing by tandem mass-spectrometry. Proc. Natl. Acad. Sci. U. S. A. 83, 6233-6237
7. Biemann, K., and Scoble, H. A. (1987) Characterization by tandem mass spectrometry of structural modifications in proteins. Science 237, 992-998
8. 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
9. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvilk, B. M., Yates, and J. R. (1999) Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17, 676-682
10. Lasonder, E., Ishihama, Y., Andersen, J. S., Vermunt, A. M., Pain, A., Sauerwein, R. W., Eling, W. M., Hall, N., Waters, A. P., Stunnenberg, H. G., and Mann, M. (2002) Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419, 537-542
11. Florens, L., Washburn, M. P., Raine, J. D., Anthony, R. M., Grainger, M., Haynes, J. D., Moch, J. K., Muster, N., Sacci, J. B., Tabb, D. L., Witney, A. A., Wolters, D., Wu, Y., Gardner, M. J., Holder, A. A., Sinden, R. E., Yates, J. R., and Carucci, D. J. (2002) A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520-526
12. Gygi, S. P., Rist, B., Griffin, T. J., Eng, J., and Aebersold, R. (2002) Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J. Proteome Res. 1, 47-54
13. 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
14. Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567
15. 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
16. 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
17. Cargile, B. J., Bundy, J. L., and Stephenson, J. L., Jr. (2004) Potential for false positive identifications from large databases through tandem mass spectrometry. J. Proteome Res. 3, 1082-1085
18. MacCoss, M. J., Wu, C. C., Yates, J. R., III (2002) Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal. Chem. 74, 5593-5599
19. Anderson, D. C., Li, W. Q., Payan, D. G., and Noble, W. S. (2003) A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J. Proteome Res. 2, 137-146
20. 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
21. Olsen, J. V., and Mann, M. (2004) Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc. Natl. Acad. Sci. U. S. A. 101, 13417-13422
22. Gentzel, M., Kocher, T., Ponnusamy, S., and Wilm, M. (2003) Preprocessing of tandem mass spectrometric data to support automatic protein identification. Proteomics 3, 1597-1610
23. Venable, J. D., Dong, M. Q., Wohlschlegel, J., Dillin, A., and Yates, J. R., III (2004) Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 1, 39-45
24. 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
25. McLafferty, F. W., Fridriksson, E. K., Horn, D. M., Lewis, M. A., and Zubarev, R. A. (1999) Techview: biochemistry. Biomolecule mass spectrometry. Science 284, 1289-1290
26. Horn, D. M., Zubarev, R. A., and McLafferty, F. W. (2000) Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 97, 10313-10317
27. 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
28. Kjeldsen, F., Haselmann, K. F., Budnik, B. A., Jensen, F., and Zubarev, R. A. (2002) Dissociative capture of hot (3-13 eV) electrons by polypeptide polycations: an efficient process accompanied by secondary fragmentation. Chem. Phys. Lett. 356, 201-206
29. Zubarev, R. A., Hakansson, P., and Sundqvist, B. (1996) Accuracy requirements for peptide characterization by monoisotopic molecular mass measurements. Anal. Chem. 68, 4060-4063
30. Jensen, O. N., Podtelejnikov, A., and Mann, M. (1996) Delayed extraction improves specificity in database searches by matrix-assisted laser desorption/ionization peptide maps. Rapid Commun. Mass Spectrom. 10, 1371-1378
31. Clauser, K. R., Baker, P., and Burlingame, A. L. (1999) Role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71, 2871-2882
32. 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
33. 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
34. 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
35. -. Anal. Chem. 77, 1831-1839
36. Carr, S., Aebersold, R., Baldwin, M., Burlingame, A., Clauser, K., and Nesvizhskii, A. (2004) The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol. Cell. Proteomics 3, 531-533
37. Nesvizhskii, A. I., and Aebersold, R. (2004) Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov. Today 9, 173-181
38. 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
39. Hoffman, M., and Rychlewski, J. (1999) Searching for palindromic sequences in primary structure of proteins. Comp. Meth. Sci. Tech. 5, 21-24
40. Giel-Pietraszuk, M., Hoffmann, M., Dolecka, S., Rychlewski, J., and Barciszewski, J. (2003) Palindromes in proteins. J. Protein Chem. 22, 109-113
41. Preissner, R., Goede, A., Michalski, E., and Frommel, C. (1997) Inverse sequence similarity in proteins and its relation to the three-dimensional fold. FEBS Lett. 414, 425-429