Proteomics shotgun

Wolters, D. A. Washburn, M. P. Yates, J. R., 3rd. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 2001, 73, 5683-5690. [Pg.224]

Wu, C. C. MacCoss, M. J. Shotgun proteomics tools for the analysis of complex biological systems. Curr. Opin. Mol. Ther. 2002, 4, 242-250. [Pg.225]

VerBerkmoes, N. C. Hervey, W. J. Shah, M. Land, M. Hauser, L. Larimer, F. W. Van Berkel, G. J. Goeringer, D. E. Evaluation of shotgun proteomics for identification of biological threat agents in complex enviromental matrices Experimental simulations. Anal. Chem. 2005,27, 923-932. [Pg.276]

Cargile, B.J., Talley, D.L., Stephenson, J.L., Jr. (2004b). Immobilized pH gradients as a first dimension in shotgun proteomics and analysis of the accuracy of pi predictability of peptides. Electrophoresis 25, 936-945. [Pg.256]

Nesvizhskii, A.I., Aebersold, R. (2005). Interpretation of shotgun proteomics data the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440. [Pg.258]

Skipp, P., Robinson, J., O Connor, C.D., Clarke, I.N. (2005). Shotgun proteomic analysis of Chlamydia trachomatis. Proteomics 5, 1558-1573. [Pg.258]

Liu, H., Sadygov, R.G., Yates, J.R, III (2004). A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193 4201. [Pg.286]

Jiang X, Jiang X, Feng S, et al. Development of efficient protein extraction methods for shotgun proteome analysis of formalin-fixed tissues. J. Proteome Res. 2007 6 1038-1047. [Pg.248]

Balgley BM, Guo T, Zhao K, et al. Evaluation of archival time on shotgun proteomics of formalin-fixed and paraffin-embedded tissues. J. Proteome Res. 2009 8 917-925. [Pg.345]

APPLICATION OF SHOTGUN PROTEOMICS TO FORMALIN-FIXED AND PARAFFIN-EMBEDDED TISSUES... [Pg.347]

THE PROMISE AND CHALLENGE OF SHOTGUN PROTEOMICS IN ARCHIVAL, FORMALIN-FIXED, PARAFFIN-EMBEDDED TISSUES (FFPE)... [Pg.347]

SHOTGUN PROTEOME ANALYSIS OF MICRODISSECTED FORMALIN-FIXED BRAIN TUMOR TISSUE... [Pg.350]

This is an important observation given that plasma membrane proteins are often used as markers of disease. This experiment demonstrated that shotgun proteomic analysis could be successfully performed on microdis-sected, formalin-fixed tissues using the antigen retrieval method with a sensitivity equal to that of analysis of the soluble fraction of a fresh-frozen sample. [Pg.353]

EVALUATION OF CONFIDENCE AND REPRODUCIBILITY OF QUANTITATIVE SHOTGUN PROTEOMIC ANALYSES... [Pg.354]

We therefore sought to evaluate reproducibility of shotgun proteomics in studies of archival FFPE tissue. Because FFPE samples are more complex than non-cross-linked samples, we evaluated FFPE human liver for analytical reproducibility and confidence in protein assignments.20 This complexity strengthens the argument for using high-resolution separations to maximize analyte concentration and minimize matrix effects. In this case, we used transient capillary isotachophoresis/capillary zone electrophoresis (cITP/cZE) in place of IEF to help address this effect. cITP/cZE has a resolution superior even to cIEF (90% of identified peptides in 1 fraction, 95% in 2 fractions or less for cITP/cZE, vs. 75% and 80%, respectively, for cIEF). [Pg.356]

As part of this work, we evaluated the effect of fixation times, from Oh to 14 days, on shotgun proteomic analyses and found no significant differences (Fig. 20.8). [Pg.356]

TABLE 20.1 Summary of IHC Staining Results and Comparison with Spectral Counts Measured by Shotgun Proteomics... [Pg.358]

Figure 20.11 Coverage of protein ErbB2 by shotgun proteomic discovery of sample ...

SHOTGUN PROTEOMICS FOR THE ANALYSIS OF ARCHIVAL FFPE TISSUES... [Pg.359]

Archival tissues stored as FFPE tissue blocks represent the vast majority of tissue archives. To investigate the effect of storage on shotgun proteomic analysis of FFPE tissues, we analyzed 10 samples dating back to 1980.22 Nine leiomyomas (three from 1990, three from 1997, and three from 2002) and one... [Pg.359]

This study demonstrated that even decades-old archival FFPE tissues are amenable to shotgun proteomic profiling and yield evaluable results. [Pg.361]

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