Proteome/Proteomic analysis mass spectrometry

However, IHC as a practical method continues to evolve with increasing demands for standardization, and for true quantification of protein analytes by weight, in the context of their cellular microenvironment. Further studies combining proteomics by mass spectrometry and IHC are likely to lead to the refinement of both methods in the analysis of FFPE tissues. The end result may be the creation of a broader field that defines and quantifies protein expression at a cellular level, incorporating the advantages of the wide spectrum of proteins demonstrable by mass spectrometry and the precise localization offered by IHC. 

Mann, M., Hendrickson, R.C., and Pandey, A. 2001. Analysis of proteins and proteomes by mass spectrometry. Annual Review of Biochemistry 70, 437-473. 

M. Quadroni, Specific detection and analysis of phosphorylated peptides by mass spectrometry, in P. James, ed., Proteome Research Mass Spectrometry, Springer-Verlag, Berlin, 2000, pp. 188-206. 

A new chapter on the primary structure of proteins, which provides coverage of both classic and newly emerging proteomic and genomic methods for identifying proteins. A new section on the appHcation of mass spectrometry to the analysis of protein structure has been added, including comments on the identification of covalent modifications. 

Gauss, C., Kalkum, M., Lowe, M., Lehrach, H., and Klose, J. (1999). Analysis of the mouse proteome. (I) Brain proteins Separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation. Electrophoresis 20, 575-600. 

Williams, C., and Addona, T. A. (2000). The integration of SPR biosensors with mass spectrometry possible applications for proteome analysis. Trends Biotechnol. 18, 45-48. 

Griffin, T. J. Han, D. K. Gygi, S. R Rist, B. Lee, H. Aebersold, R. Parker, K. C. Toward a high-throughput approach to quantitative proteomic analysis Expression-dependent protein identification by mass spectrometry. J. Am. Soc. Mass. Spectrom. 2001,12,1238-1246. 

Dunlop, K. Y. Li, L. Automated Mass Analysis of low-molecular-mass bacterial proteome by liquid chromatography-electrospray ionization mass spectrometry. J. Chromatogr. A 2001, 925,123-132. 

The results for bacterial whole-cell analysis described here establish the utility of MALDI-FTMS for mass spectral analysis of whole-cell bacteria and (potentially) more complex single-celled organisms. The use of MALDI-measured accurate mass values combined with mass defect plots is rapid, accurate, and simpler in sample preparation then conventional liquid chromatographic methods for bacterial lipid analysis. Intact cell MALDI-FTMS bacterial lipid characterization complements the use of proteomics profiling by mass spectrometry because it relies on accurate mass measurements of chemical species that are not subject to posttranslational modification or proteolytic degradation. 

Electrospray (ESI) ionization mass spectrometry also plays in important role in bacterial characterization. Because it typically includes a chromatographic separation step, the approach is not considered as rapid as MALDI approaches, which do not incorporate a separation. However, compared to the times needed to grow bacteria in culture prior to analysis, the time frame is not lengthy, and the addition of chromatographic separation provides many opportunities to increase specificity. ESI/MS has been used to characterize cellular biomarkers for metabolic, genomic, and proteomics fingerprinting of bacteria, and these approaches are reported in two chapters. 

D-polyacrylamide gel electrophoresis) maps of protein mixtures is discussed. 2D PAGE is considered the classical and principal tool for protein separation—prior to mass spectrometry—to achieve the main goal of proteomics, that is, a comprehensive identification and quantification of every protein present in a complex biological sample that would allow analysis of an entire intact proteome (Wilkins et al., 1997 Righetti et al., 2001 Hamdan and Righetti, 2005). 

Schley, C., Altmeyer, M.O., Swart, R., Muller, R., Huber, C.G. (2006). Proteome analysis of Myxococcus xanthus by off-line two-dimensional chromatographic separation using monolithic poly-(styrene-divinylbenzene) columns combined with ion-trap tandem mass spectrometry. J. Proteome Res. 5, 2760-2768. 

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