Bioinformatics-based strategies for rapid microorganism identification by mass spectrometry

Johns Hopkins APL Technical Digest (Applied Physics Laboratory)

Volumn 25, Issue 1, 2004, Pages 27-37

  Demirev, Plamen A ^a   Feldman, Andrew B ^a   Lin, Jeffrey S ^a,b  

^a APL   (United States)

^b Research and Technology Development Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; MICROBIAL GENOME; PATHOGENIC BACTERIA; POST TRANSLATIONAL MODIFICATIONS (PTM);

DATABASE SYSTEMS; GENES; MASS SPECTROMETRY; MICROORGANISMS; STATISTICAL METHODS;

BIOMEDICAL ENGINEERING;

EID: 8344246222     PISSN: 02705214     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (64)

1. Anhalt, J. P., and Fenselau, C, "Identification of Bacteria Using Mass Spectrometry," Anal Chem. 47, 219-225 (1975).
2. Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., and Whitehousc, C. M., "Electrospray lonization for Mass Spectrometry of Large Biomolecules," Science 246, 64-71 (1989).
3. Tanaka, K., Waki, H., Ido, Y., Akita, S., and Yoshida, Y., "Protein and Polymer Analysis up to m/z 100,000 by Laser lonization Time-of-Flight Mass Spectrometry," Rapid Commun. Mass Spectrom. 2, 151-153(1988).
4. Karas, M., and Hillenkamp, F., "Laser Desorption lonization of Proteins with Molecular Masses Exceeding 10,000 Daltons," Anal. Chem. 60(20), 2299-2301 (1988).
5. Bryden, W. A., Benson, R. C., Ecelberger, S. A., Phillips, T. E., Cotter, R. J., and Fenselau, C., "The Tiny-TOF Mass-Spectrometer for Chemical and Biological Sensing," Johns Hopkins APL Tech. Dig. 16,296-310(1995).
6. Claydon, M. A., Davey, S. N., Edwards Jones, V., and Gordon, D. B., "The Rapid Identification of Intact Microorganisms Using Mass Spectrometry," Nat. Biotechnol. 14, 1584-1586 (1996).
7. Holland, R. D., Wilkes, J. G., Raffi, F., Sutherland, J. B., Persons, C. C., et al., "Rapid Identification of Intact Whole Bacteria Based on Spectral Patterns Using Matrix-Assisted Laser Desorption/Ionization with Time-of-Flight Mass Spectrometry," Rapid Commun. Mass Spectrom. 10, 1227-1232 (1996).
8. Krishnamurthy, T., Ross, P. L., and Rajamani, U., "Detection of Pathogenic and Non-Pathogenic Bacteria by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry," Rapid Commun. Mass Spectrom. 10, 883-888 (1996).
9. Welham, K.J., Domin, M. A., Scannell, D. E., Cohen, E., and Ashton, D. S., "The Characterization of Micro-Organisms by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry," Rapid Commun. Mass Spectrom. 12, 176-180 (1998).
10. Wang, Z. P., Russon, L, Li, L, Roser, D. C., and Long, S. R., "Investigation of Spectral Reproducibility in Direct Analysis of Bacteria Proteins by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry," Rapid Commun. Mass Spectrom. 12, 456-464 (1998).
11. Arnold, R. J., and Reilly, J. P., "Fingerprint Matching of E. coli Strains with Matrix-Assisted Laser Desorption lonization Time-of-Flight Mass Spectrometry of Whole Cells Using a Modified Correlation Approach," Rapid Commun. Mass Spectrom. 12, 630-636 (1998).
12. Thomas, J. J., Falk, B., Fenselau, C., Jackman, J., and Ezzell, J., "Viral Characterization by Direct Analysis of Capsid Proteins," Anal. Chem. 70, 3863-3867 (1998).
13. Winkler, M. A., Uher, J., and Cepa, S., "Direct Analysis and Identification of Helicobacter and Campylobacter Species by MALDI-TOF Mass Spectrometry," Anal. Chem. 71, 3416-3419 (1999).
14. Jarman, K. H., Cebula, S. T., Saenz, A. J., Petersen, C. E., Valentine, N. B., et al., "An Algorithm for Automated Bacterial Identification Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry," Anal. Chem. 72, 1217-1223 (2002).
15. Scholl, P. F., Leonardo, M. A., Rule, A. M., Carlson, M. A., Antoine, M. D., and Buckley, T. J., "The Development of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for the Detection of Biological Warfare Agent Aerosols," Johns Hopkins APL Tech. Dig. 20, 343-351(1999).
16. Fenselau, C., and Demirev, P., "Characterization of Intact Microorganisms by MALDI Mass Spectrometry," Mass Spectrom. Rev. 20, 157-171 (2001).
17. Lay, J., "MALDI-TOF Mass Spectrometry of Bacteria," Moss Spectrom. Rev. 20, 172-194 (2001).
18. Demirev, P., Ho, Y. P., Ryzhov, V., and Fenselau, C., "Microorganism Identification by Mass Spectrometry and Protein Database Searches," Anal. Chem. 71, 2732-2738 (1999).
19. Pineda, F., Lin, J. S., Fenselau, C., and Demirev, P., "Testing the Significance of Microorganism Identification by Mass Spectrometry and Proteome Database Search," Anal. Chem. 72, 3739-3744 (2000).
20. Demirev, P., Lin, J. S., Pineda, F. J., and Fenselau, C., "Bioinformatics and Mass Spectrometry for Microorganism Identification: Proteome-Wide Post-Translational Modifications and Database Search Algorithms for Characterization of Intact H. pylori," Anal. Chem. 73, 4566-4573 (2001).
21. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M. C., Estreicher, A., et al., "The SWISS-PROT Protein Knowledgebase and Its Supplement TrEMBL," Nucl. Acids Res. 31(1), 365-370 (1 Jan 2003).
22. ExPASy Molecular Biology Server Web site, http://expasy.ch/.
23. Institute for Genomic Research Web site, http:// www.tigr.org.
24. Read, T. D., Peterson, S. N., Tourasse, N., Baillie, L. W., Paulsen, I. T., et al., "The Genome Sequence of Bacillus anthracis Ames and Comparison to Closely Related Bacteria," Nature 423, 81-86 (2003).
25. Ivanova, N., Sorokin, A., Anderson, I., Galleron, N., Candelon, B., et al., "Genome Sequence of Bacillus cereus and Comparative Analysis with Bacillus anthracis," Nature 423, 87-91 (2003).
26. Marra, M. A., Jones, S. J., Astell, C. R., Holt, R. A., Brooks-Wilson, A. R., et al., "The Genome Sequence of the SARS-Associated Coronavirus," Science 300, 1399-1404 (2003).
27. Lee, S. W., Berger, S. J., Martinovic, S., Pasa-Tolic, L., Anderson, G. A., et al, "Direct Mass Spectrometric Analysis of Intact Proteins of the Yeast Large Ribosomal Subunit Using Capillary LC/FTICR," Proc. Nat. Acad. Sci. 99, 5942-5947 (2002).
28. Jones, J. J., Stump, M. J., Fleming, R. C., Lay, J. O., and Wilkins, C. L., "Investigation of MALDI-TOF and FT-MS Techniques for Analysis of Escherichia coli Whole Cells," Anal. Chem. 75, 1340-1347 (2003).
29. Stump, M. J., Jones, J. J., Fleming, R. C., Lay, J. O., and Wilkins, C. L., "Use of Double-Depleted C-13 and N-15 Culture Media for Analysis of Whole Cell Bacteria by MALDI Time-of-Flight and Fourier Transform Mass Spectrometry," J. Am. Soc. Mass Spectrom. 14, 1306-1314 (2003).
30. Gonzales, T., and Baudouy, J. R., "Bacterial Aminopeptidases: Properties and Functions," FEMS Microbiol. Rev. 18, 319-344 (1996).
31. http://infobacter. jhuapl.edu.
32. Pineda, F., Antoine, M., Demirev, P., Feldman, A., Jackman, J., et al., "Rapid Microorganism Identification by MALDI Mass Spectrometry and Model-Derived Ribosomal Protein Biomarkers," Anal. Chem. 75, 3817-3822(2003).
33. Arnold, R. J., and Reilly, J. P., "Observation of E. coli Ribosomal Proteins and Their Posttranslational Modifications by Mass Spectrometry," Anal. Biochem. 269, 105-112 (1999).
34. Wang, Z. P., Dunlop, K., Long, S. R., and Li, L., "Mass Spectrometric Methods for Generation of Protein Mass Database Used for Bacterial Identification," Anal. Chem. 74, 3174-3182 (1 Jul 2002).
35. Williams, T. L., Leopold, P., and Musser, S., "Automated Postprocessing of Electrospray LC/MS Data for Profiling Protein Expression in Bacteria," Anal. Chem. 74(22), 5807-5813 (15 Nov 2002).
36. Karlin, S., Campbell, A. M., and Mrazek, J., "Comparative DNA Analysis Across Diverse Genomes," Ann. Rev. Genetics 32, 185-225 (1998).
37. Demirev, P. A., Feldman, A. B., Lin, J. S., Pineda, F. J., and Resch, C. L., "Microorganism Identification by Mass Spectrometry and Bioinformatics-Generated Biomarker Databases," in Proc. 51st Ann. Conf. of the ASMS, CD-ROM, Montreal, Canada (Jun 2003).
38. Sharp, P. M., and Li, W. H., "The Codon Adaptation Index: A Measure of Directional Synonymous Codon Usage Bias, and Its Potential Applications," Nucl. Acids Res. 15, 1281-1295 (1987).
39. Perrot, M., Sagliocco, F., Mini, T., Monribot, C., Schneider, U., et al., "Two-Dimensional Gel Protein Database of S. cerevisiae" Electrophoresis 20, 2280-2298 (Aug 1999).
40. Smith, R. D., Anderson, G. A., Lipton, M. S., Pasa-Tolic, L., Shen, Y., et al., "An Accurate Mass Tag Strategy for Quantitative and High-Throughput Proteome Measurements," Proteomics 2, 513-523 (2002).
41. Hunter, T. C., Andon, N. L., Koller, A., Yates, J. R., and Haynes, P. A., "The Functional Proteomics Toolbox: Methods and Applications," J. Chromatogr. B782, 165-181 (2002).
42. European Molecular Biology Open Software Suite Web site, http:// www.hgmp.mrc.ac.uk/Software/EMBOSS/
43. Mortz, E., O'Connor, P., Roepstorff, P., Kelleher, N., Wood, T., et al., "Sequence Tag Identification of Intact Proteins by Matching Tandem Mass Spectral Data Against Sequence Data Bases," Proc. Nat. Acad. Sci. 93, 8264-8267 (1999).
44. Zubarev, R., Kelleher, N., and McLafferty, F. W., "Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process,";. Am. Chem. Soc. 120, 3265-3266 (1998).
45. Li, W., Hendrickson, C., Emmett, M., and Marshall, A. G., "Identification of Intact Proteins in Mixtures by Alternated Capillary Liquid Chromatography Electrospray Ionization and LC ESI Infrared Multiphoton Dissociation Fourier Transform Ion Cyclotron Resonance Mass Spectrometry," Anal. Chem. 71, 4397-4402 (1999).
46. Xiang, F., Anderson, G. A., Veenstra, T., Lipton, M., and Smith, R. D., "Characterization of Microorganisms and Biomarker Development from Global ESI-MS/MS Analyses of Cell Lysares," Anal. Chem. 72, 2475-2481 (2000).
47. Meng, F. Y., Cargile, B. J., Miller, L. M., Forbes, A. J., Johnson, J. R., and Kelleher, N., "Informatics and Multiplexing of Intact Protein Identification in Bacteria and the Archaea," Nat. Biotechnol. 19(10), 952-957 (Oct 2001).
48. Taylor, G. K., Kim, Y. B., Forbes, A. J., Meng, F. Y., McCarthy, R., and Kelleher, N. L., "Web and Database Software for Identification of Intact Proteins Using 'Top Down' Mass Spectrometry," Anal. Chem. 75(16), 4081-4086 (15 Aug 2003).
49. Cargile, B., McLuckey, S. A., and Stephenson, J. L., "Identification of Bacteriophage MS2 Coat Protein from E. coli Lysates via Ion Trap Collisional Activation of Intact Protein Ions," Anal. Chem. 73,1277-1285 (2001).
50. Demirev, P., Ramirez, J., and Fenselau, C., "Tandem Mass Spectrometry of Intact Proteins for Characterization of Biomarkers from Bacillus cereus T Spores," Anal. Chem. 73, 5725-5731 (2001).
51. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., et al, "Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs," Nucleic Acids Res. 25, 3389-3402 (1997).
52. Wilkins, M. R., Appel, R. D., Hochstrasse, D. F., and Williams, K. L. (eds.), Proteome Research: New Frontiers in Functional Genomics, Springer-Verlag, New York (1997).
53. Liebler, D. C., Introduction to Proteomics: Tools for the New Biology, Humana Press (2001).
54. Aebersold, R., and Mann, M., "Mass Spectrometry-Based Proteomics," Nature 422(6928), 198-207 (13 Mar 2003).
55. Warscheid, B., and Fenselau, C., "Characterization of Bacillus Spore Species and Their Mixtures Using Postsource Decay with a CurvedField Reflectron," Anal. Chem. 75, 5608-5617 (2003).
56. Warscheid, B., Jackson, K., Sutton, C., and Fenselau, C., "MALDI Analysis of Bacilli in Spore Mixtures by Applying a Quadrupole Ion Trap Time-of-Flight Tandem Mass Spectrometer," Anal. Chem. 75, 5608-5617 (2003).
57. Yao, Z., Demirev, P., and Fenselau, C., "Mass Spectrometry-Based Proteolytic Mapping for Rapid Virus Identification," Anal. Chem. 74, 2529-2534 (2002).
58. English, R. D., Warscheid, B., Fenselau, C., and Cotter, R. J., "Bacillus Spore Identification via Proteolytic Peptide Mapping with a Miniaturized MALDI TOF Mass Spectrometer," Anal. Chem. 75, 6886-6893 (2003).
59. Krokhin, O., Li, Y., Andonov, A., Feldmann, H., Flick, R., et al., "Mass Spectrometric Characterization of Proteins from the SARS Virus," Mol, Cell. Proteomics 2, 346-356 (2003).
60. Elhanany, E., Barak, R., Fisher, M., Kobiler, D., and Altboum, Z., "Detection of Specific Bacillus anthracis Spore Biomarkers by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spcctrometry," Rapid Comm. Mass Spectrom, 15, 2110-2116 (2001).
61. Hathout, Y., Setlow, B., Cabrcra-Martinez, R. M., Fenselau, C, and Setlow, P., "Small, Acid-Soluble Proteins as Biomarkers in Mass Spectrometry Analysis of Bacillus Spores," Appl. Environ. Microbiol. 69, 1100-107 (2001).
62. Cornish, T. J., und Bryden, W. A., "Miniature Time-of-Flight Mass Spectrometer for a Field-Portable Biodetection System," Johns Hopkins APL Tech. Dig. 20(3), 335-342 (1999).
63. McLoughlin, M. P., Allmon, W. R., Anderson, C. W., Carlson, M. A., DeCicco, D. J., and Evancich, N. H., "Development of a FieldPortable Time-of-Flight Mass Spectrometer System," Johns Hopkins APL Tech. Dig. 20(3), 326-332 (1999).
64. Ko, H. W., "Biomédical and Biochemical Technology at APL," Johns Hopkins APL Tech. Dig. 24(1), 41-51 (2003).