Improving mass and liquid chromatography based identification of proteins using Bayesian scoring

Journal of Proteome Research

Volumn 4, Issue 6, 2005, Pages 2174-2184

  Chen, Sharon S ^a,b   Deutsch, Eric W ^b   Yi, Eugene C ^b   Li, Xiao Jun ^b   Goodlett, David R ^b,d   Aebersold, Ruedi ^b,c  

^a University of Washington   (United States)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^c UNIVERSITY OF ZURICH   (Switzerland)

^d UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Electrospray ionization; HPLC; m z; MS; MS MS; Tandem mass spectrometry; TOF

Indexed keywords

PEPTIDE; PROTEIN;

ALGORITHM; ANALYTIC METHOD; ARTICLE; AUTOANALYSIS; BAYES THEOREM; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SCORING SYSTEM; TANDEM MASS SPECTROMETRY; YEAST;

ALGORITHMS; BAYES THEOREM; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CHROMATOGRAPHY, LIQUID; DATABASES, PROTEIN; FUNGAL PROTEINS; MASS SPECTROMETRY; MODELS, STATISTICAL; PEPTIDES; PROTEINS; PROTEOMICS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; YEASTS;

EID: 29144536205     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr050251c     Document Type: Article

References (24)

1. Strittmatter, E. F., et al. Proteome Analyses Using Accurate Mass and Elution Time Peptide Tags with Capillary LC Time-of-Flight Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2003, 14, 980-991.
2. Pasa-Tolic, L., et al. Proteomic analyses using an accurate mass and time tag strategy. BioTechniques 2004, 37 (4), 621-639.
3. Goodlett, D. R.; Bruce, J. E.; Anderson, G. A.; Rist, B.; Pasa-Tolic, L.; Fiehn, O.; Smith, R. D.; Aebersold, R. Protein Identification with a Single Accurate Mass of a Cysteine-Containing Peptide and Constrained Database Searching. Anal. Chem. 2000, 72, 1112-1118.
4. Lipton, M. S., et al. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc. Natl. Acad. Sci. 2002, 99(17), 11049-11054.
5. Smith, R. D., et al. An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2002, 2, 513-523.
6. Petritis, K.; Kangas, L. J.; Ferguson, P. L.; Anderson, G. A.; Pasa-Tolic, L.; Lipton, M. S.; Auberry, K. J.; Strittmatter, E. F.; Shen, Y.; Zhao, R.; Smith, R. D. Use of Artificial Neural Networks for the Accurate Prediction of Peptide Liquid Chromatography Elution Times in Proteome Analyses. Anal. Chem. 2003, 75 (5), 1039-1048.
7. Wall, D., S. J. Parus, and D. M. Lubman, Three-dimensional protein map according to pI, hydrophobicity, and molecular mass. J. Chromatogr. B 2002, 774, 53-58.
8. Conrads, T. P.; Anderson, G. A.; Veenstra, T. D.; Pasa-Tolic, L.; Smith, R. D. Utility of Accurate Mass Tags for Proteome-Wide Protein Identification. Anal. Chem. 2000, 72, 3349-3354.
9. Strittmatter, E. F.; Rodriguez, N.; Smith, R. D. High Mass Measurement Accuracy Determination for Proteomics Using Multivariate Regression Fitting: Application to Electrospray Ionization Time-Of-Flight Mass Spectrometry. Anal. Chem. 2003, 75, 460-468.
10. Pasa-Tolic, L., et al., Increased Proteome Coverage for Quantitative Peptide Abundance Measurements Based upon High Performance Separations and DREAMS FTICR Mass Spectrometry. Am. Soc. Mass Spec. 2002, 13, 954-963.
11. Smolka, M. B., et al. Optimization of the isotope-coded affinity tag-labeling for quantitative proteome analysis. Anal. Biochem. 2001, 297, 25-31.
12. Schultz, M. C. Chromatin assembly in yeast cell-free extracts. Methods 1999, 17, 161-172.
13. Yi, E. C., et al. A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine operation. Rapid Comm. Mass. Spec. 2003, 17, 2093-2098.
14. Sherman, J. Identification of peptide distribution by an analytic template function. PhD Dissertation, 2005.
15. Eng, J.; McCormack, A. L.; Yates, J. R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Am. Soc. Mass. Spec. 1994, 5, 976-989.
16. Han, D. K., et al. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass Spectrometry. Nat. Biotechnol. 2001, 19, 946-951.
17. Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75, 4646-4658.
18. Flory, M. R., et al. An SMC-domain protein in fission yeast links telomeres to the meiotic centrosome. Mol. Cell. 2004, 16, 619-630.
19. Ranish, J. A., et al. Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat. Genet. 2004, 36 (7), 717-713.
20. Ranish, J. A., et al. The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 2003, 33 (3), 349-355.
21. Chen, S. S.; Aebersold, R. LC-MS solvent composition monitoring and chromatography alignment using mobile phase tracer molecules. J. Chromatogr. B. 2005, in press.
22. Zubarev, R. A.; Hakansson, P.; Sundqvist, B. Accuracy requirements for peptide characterization by monoisotopic molecular mass measurements. Anal. Chem. 1996, 68, 4060-4063.
23. Hopp, T. P.; Woods, K. R. Prediction of protein antigenic determinants from amino acid sequences. Proc. Natl. Acad. Sci. 1981, 78 (6), 3824-3828.
24. Norbeck, A. D., et al. The utility of accurate mass and LC elution time information in the analysis of complex proteomes. J. Am. Soc. Mass. Spectrom. 2005, 16, 1239-1249.