Mass protein analysis

Domon B, Aebersold R (2006) Mass spectrometry and protein analysis. Science 312 212-217... 

The ultimate goal of microarray-based expression analysis is to acquire a comprehension of the entire cellular process, in order to exploit and to standardize the multidi-menisional relations between genotype and phenotype. However, an increasingly important parameter, which has not yet been substantially taken into account, is the role of cellular translation. This means that mRNA expression data need to be correlated with the assortment of proteins actually present in the cell. One approach is based on the use of microarrays containing double-stranded DNA probes for the analysis of DNA-protein interaction and, thus, the detection and identification of DNA-binding proteins by means of fluorescence [130] or mass spectrometry analysis [131]. Moreover, substantial efforts are currently under way to develop protein, antibody, or even cell arrays, applicable to the cor-... 

Bolton, J. L. Le Blanc, J. C. Y. Siu, K. W. M. Reaction of quinone methides with proteins analysis of myoglobin adduct formation by electrospray mass spectrometry. Biol. Mass... 

Hathout, Y. Setlow, B. Cabrera-Martinez, R. M. Fenselau, C. Small, acid-soluble proteins as biomarkers in mass spectrometry analysis of Bacillus spores. Appl. Environ. Microbiol. 2003,69,1100-1107. 

These columns have been used for separation of proteins of over 200 kDa MW in our experiments as shown by analysis using a ID gel. In addition, columns with larger particle sizes have been used to separate proteins of over 400 kDa (55-56). The NPS RP-HPLC method provides a liquid phase method for separating large intact proteins for further analysis. More specifically, it provides a means of separating proteins for interfacing to mass spectrometric analysis. 

Field, H.I., Fenyo, D., Beavis, R.C. (2002). RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics 2, 36 17. 

Peng, J., Elias, J.E., Thoreen, C.C., Licklider, L.J., Gygi, S.P. (2003). Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC—MS/MS) for large-scale protein analysis the yeast proteome. J. Proteome Res. 2, 43-50. 

Von Haller, P.D., Yi, E., Donohoe, S., Vaughn, K., Keller, A., Nesvizhskii, A.I., Eng, J., Li, X.J., Goodlett, D.R., Aebersold, R., Watts, J.D. (2003). The Application of New Software Tools to Quantitative Protein Profiling Via Isotope-coded Affinity Tag (ICAT) and Tandem Mass Spectrometry II. Evaluation of Tandem Mass Spectrometry Methodologies for Large-Scale Protein Analysis, and the Application of Statistical Tools for Data Analysis and Interpretation. Mol. Cell. Proteomics 2, 428 -42. 

Lee, S.W., Berger, S.J., Martinovic, S., Pasa-Tolic, L., Anderson, G.A., Shen, Y., Zhao, R., Smith, R.D. (2002). Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR. Proc. Natl. Acad. Sci. USA 99, 5942-5947. 

Joubert-Caron R et al. Protein analysis by mass spectrometry and sequence database searching a proteomic approach to identify human lymphoblastoid cell line proteins. Electrophoresis 2000 21 2566— 2575. 

Wattiez R et al. Human bronchoalveolar lavage fluid protein two-dimensional database study of interstitial lung diseases. Electrophoresis 2000 21 2703-2712. Yanagida M et al. Matrix assisted laser desorption/ionization-time of flight-mass spectrometry analysis of proteins detected by anti-phosphotyrosine antibody on two-dimensional-gels of fibrolast cell lysates after tumor necrosis factor-alpha stimulation. Electrophoresis 2000 21 1890-1898. 

Verma R et al. Proteasomal proteomics identification of nucleotide-sensitive pro-teasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol Biol Cell 2000 11 3425-3439. 

Compare findings with Western blot or mass spectrometry analysis to validate the quantitative measurement using protein-embedded bar code-based image analysis. 

Chong BE, Lubman DM, Miller FR, et al. Rapid screening of protein profiles of human breast cancer cell lines using non-porous reversed-phase high performance liquid chromatography separation with matrix-assisted laser desorption/ionization time-of-flight mass spectral analysis. Rapid Commun. Mass Spectrom. 1999 13 1808-1812. 

ICAT reagents can be used to compare two different samples by mass spec analysis. For instance, one cell population can be treated with a drug candidate, while another one remains untreated and acts as a control. Alternatively, one cell population can represent a disease state and the control population is the normal cell line. After cell lysis, the proteins in each... 

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