Proteomic profiles

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. 

Tyan, Y.C., Wu, H.Y., Lai, W.W., Su, W.C., Liao, PC. (2005b). Proteomic profiling of human pleural effusion using two-dimensional nano liquid chromatography tandem mass spectrometry. J. Proteome Res. 4, 1274-1286. 

Wang, H., Clouthier, S.G., Galchev, V., Misek, D.E., Duffner, U., Min, C.K., Zhao, R., Tra, J., Omenn, G.S., Ferrara, J.L., Hanash, S.M. (2005). Intact-protein-based high-resolution three-dimensional quantitative analysis system for proteome profiling of biological fluids. Mol. Cell. Proteomics 4, 618-625. 

Proteome profiling allows quantitative and global examination of the changes in protein expression in different strains or cells under different conditions. Two-dimensional gel... 

Han, M.-J., Jeong, K.J., Yoo, J.-S. and Lee, S.Y. (2003) Engineering Escherichia coli for increased productivity of serine-rich proteins based on proteome profiling. Applied and Environmental Microbiology, 69, 5772-5781. 

Ostergaard M et al. Proteome profiling of bladder squamous cell carcinomas identification of markers that define their degree of differentiation. Cancer Res 1997 57 4111 117. 

Voss Tet al. Correlation of clinical data with proteomics profiles in 24 patients with B-cell chronic lymphocytic leukemia. Int J Cancer 2001 91 180-186. 

Prieto DA, Hood BL, Darfler MM, et al. Liquid TissueTM proteomic profiling of formalin-fixed tissues. BioTechniques 2005 38 S32-S35. 

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

Wei, Y., and Chen, S.S. (2005) Mass spectrometry-based quantitative proteomic profiling. Briefings in functional genomics and proteomics 4, 1-12. 

Hanash, S.M., and L.M. Baretta, "Operomics Integrated Genomic and Proteomic Profiling of Cells and Tissues," Briefings Fund. Genomics Proteomics, 1, 10-22 (2002). 

Merrick, B. A. and Bruno, M. E., Genomic and proteomic profiling for biomarkers and signature profiles of toxicity, Curr. Opin. Mol. Ther., 6, 600, 2004. 

Global proteomic profiling by MS is gaining significant attention as a tool for discovering disease biomarkers. Two basic approaches have been explored. With the first, MS analysis is performed with a material from a specific disease condition and the mass spectra are compared to those of normal individuals or related disease conditions. SELDI-TOF MS gained popularity in this area because of its simplicity and the requirement for only small amounts of samples.38"13 In MS-pattem based disease categorization, the mass spectral patterns are considered reflective of the proteins present in samples from distinct clinical conditions. 

In addition to MALDI-TOF and LC-MS/MS, SELDI-TOF-MS can also be used to determine expression profiling of various biological samples, such as serum or plasma for early detection of infection. Serum proteomic profiling assay, for instance, has been used to distinguish patients with acute SARS (severe acute respiratory syndrome) from patients with fever and influenza with 100% accuracy [16]. A major limitation of SELDI-TOF-MS, however, is that it cannot be used for direct amino acid sequence identification of the biomarker proteins, necessitating further sample fractionation and protein purification. 

V. G. DelVecchio, J. P. Connolly, T. G. Alefantis, A. Walz, M. A. Quan, G. Patra, J. M. Ashton, J. T. Whittington, R. D. Chafin, X. Liang, P. Grewal, A. S. Khan, and C. V. Mujer. 2006. Proteomic Profiling and Identification of Immunodominant Spore Antigens of Bacillus Anthracis, Bacillus Cereus and Bacillus Thuringiensis. Appl. Environ. Microbiol, 72(2006) 6355-6363. 

Nishizuka, S., Charboneau, L., Young, L., Major, S., Reinhold, W.C., Waltham, M., Kouros-Mehr, H., Bussey, K.J., Lee, J.K., Espina, V., Munson, RJ., Petricoin, E., Liotta, L.A., and Weinstein, J.N., Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays, Proc. Natl. Acad. Sci. USA, 24, 14229-14234, 2003. 

The study published by Hennessey et al. (46) concluded that proteomic profiles of frozen samples were consistent in the absence of microdissection. However, several critical points need to be considered first, the fact that proteomic profiles did not change between biologic replicates might simply mean that the intra-sample variability of the selected proteins was probably low, so that regardless of where the sample was taken the tumor looked the... 

M. N. Gandy, A. W. Debowski, and K. A. Stubbs, A general method for affinity-based proteomic profiling of exo-a-glucosidases, Chem. Commun., 47 (2011) 5037-5039. 

Osman AM et al (2010) Proteome profiling of mouse embryonic stem cells to define markers for cell differentiation and embryo-toxicity. Reprod Toxicol 30 322-332. doi S0890-6238(10)00193-0(pii)10.1016/j. reprotox.2010.05.084... 

Fig. 3. Advanced protocol of 2D-DIGE for a number of protein samples larger than the available fluorescent dyes. The internal control sample and individual samples are labeled with CyS and CyS, respectively. The differently labeled protein samples are mixed together and separated on individual gels. After gel electrophoresis, the gels are scanned with laser at the appropriate wavelength for CyS and CyS. As all gel scans generate the CyS image that represents the proteomic profile of the internal control sample, gel-to-gel variations are compensated by normalizing CyS images with CyS images for each gel. We can compare more protein samples than the available fluorescent dyes.

DNA Microarrays for Transcription Profiling Tumor Tissue Microarray and Proteomic Profiling Of Protein Kinases Molecular Profiling for Cancer Therapeutics New Guidelines For Reporting Tumor Marker Studies Conclusions References... 

Key Words Breast cancer prognosis transcriptional profiling proteomic profiling tissue array chemosensitivity prediction... 

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