Protein Identification from Tandem Mass Spectra by Database Searching

Methods in Molecular Biology

Volumn 694, Issue , 2011, Pages 119-138

  Edwards, Nathan J ^a  

^a GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

MS MS spectra; Peptide identification; Protein identification; Protein sequence databases; Search engine

Indexed keywords

AMINO ACID SEQUENCE; EXTRACTION; PROTEIN ANALYSIS; SEARCH ENGINE; SEQUENCE DATABASE; TANDEM MASS SPECTROMETRY; ALGORITHM; ARTICLE; CHEMISTRY; INSTRUMENTATION; ISOTOPE LABELING; METHODOLOGY; MOLECULAR GENETICS; MOLECULAR WEIGHT; PROTEIN DATABASE;

PEPTIDE; PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; DATABASES, PROTEIN; ISOTOPE LABELING; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; PEPTIDES; PROTEINS; SEARCH ENGINE; TANDEM MASS SPECTROMETRY;

MLCS; MLOWN;

EID: 79952118131     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-977-2_9     Document Type: Chapter

References (24)

1. Aebersold, R. and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198–207.
2. Deutsch, E. W., Lam, H., and Aebersold, R. (2008) Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiological Genomics 33, 18–25.
3. Johnson, R., Davis, M., Taylor, J., and Patterson, S. (2005) Informatics for protein identification by mass spectrometry. Methods 35, 223–236.
4. Maccoss, M. (2005) Computational analysis of shotgun proteomics data. Current Opinion in Chemical Biology 9, 88–94.
5. McDonald, W. H. and Yates, J. R. (2003) Shotgun proteomics: integrating technologies to answer biological questions. Current Opinion in Molecular Therapeutics 5, 302–309.
6. Nesvizhskii, A. I. (2007) Mass Spectrometry Data Analysis in Proteomics, volume 367 of Methods in Molecular Biology, chapter Protein Identification by Tandem Mass Spectrometry and Sequence Database Searching, 87–119. Humana Press, Totowa, NJ.
7. 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. Nature Methods 1, 195–202.
8. Bafna, V. and Edwards, N. (2003) On de novo interpretation of tandem mass spectra for peptide identification. In RECOMB ’03: Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology, 9–18. ACM Press, New York.
9. Chen, T., Kao, M. Y., Tepel, M., Rush, J., and Church, G. M. (2001) A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. Journal of Computational Biology 8, 325–337.
10. Frank, A. and Pevzner, P. (2005) Pepnovo: de novo peptide sequencing via probabilistic network modeling. Analytical Chemistry 77, 964–973.
11. Taylor, A. and Johnson, R. S. (1997) Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Communications in Mass Spectrometry 11, 1067–1075.
12. Mann, M. and Wilm, M. (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Analytical Chemistry 66, 4390–4399.
13. Tabb, D. L., Ma, Z.-Q., Martin, D. B., Ham, A.-J. L., and Chambers, M. C. (2008) DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. Journal of Proteome Research 7, 3838–3846.
14. Tanner, S., Shu, H., Frank, A., Wang, L. C., Zandi, E., Mumby, M., Pevzner, P. A., and Bafna, V. (2005) Inspect: identification of post-translationally modified peptides from tandem mass spectra. Analytical Chemistry 77, 4626–4639.
15. Dass, C. (2001) Principles and Practice of Biological Mass Spectrometry. John Wiley & Sons, Inc., New York.
16. 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.
17. 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. Journal of the American Society of Mass Spectrometry 5, 976–989.
18. Craig, R. and Beavis, R. C. (2004) Tandem: matching proteins with tandem mass spectra. Bioinformatics 20, 1466–1467.
19. 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. Journal of Proteome Research 3, 958–964.
20. Kersey, P. J., Duarte, J., Williams, A., Karavidopoulou, Y., Birney, E., and Apweiler, R. (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics 4, 1985–1988.
21. The Uniprot Consortium (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Research 38, D142–D148.
22. Edwards, N. J. (2007) Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Molecular Systems Biology 3, 102.
23. Keller, A., Eng, J., Zhang, N., Li, X.-J. J., and Aebersold, R. (2005) A uniform proteomics MS/ MS analysis platform utilizing open XML file formats. Molecular Systems Biology 1, 2005.0017.
24. Kessner, D., Chambers, M., Burke, R., Agus, D., and Mallick, P. (2008) ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534–2536.