Spectrometric Proteome Analysis

One major shortcoming in the apphcation of the combination of 2D-gel electrophoresis with mass spectrometry is the loss of information about specific protein-protein interactions and molecular recognition processes due to the denaturating electrophoretic conditions. At present, only a few, but promising, attempts have been made to directly analyse interactions in proteome studies [19, 141, 150]. Recently, a new approach for the identification of affinity bound proteins by proteolytic generation and mass spectrometric analysis of its antibody-bound 

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Site offers mMass program that is an open source package of simple tools, written mainly in Phyton and dedicated to mass spectrometric data analysis. It can also be used for protein sequence handling and other proteomic tasks. 

Jensen, O. N. 1999. Sample preparation methods for mass spectrometric peptide mapping directly from 2-DE gels. In 2-D Proteome Analysis Protocols, Link, A. I, ed., Humana Press (Totowa, New Jersey), 513-530. 

MALDI and ESI represent the predominant ionization techniques in mass spectrometry-based proteomics, as recognized by the Nobel Prize in chemistry in 2002. MALDI is mainly used to volatize and ionize simple polypeptide samples for mass spectrometric (MS) analysis at high speed. The analysis of more complex peptide mixtures is usually conducted via ESI mass spectrometry (ESI MS) coupled online with a high-pressure liquid chromatography (HPLC) system to concentrate and separate peptides prior to MS analysis. 

Lee, K.R. Lin, X. Park, D.C. Eslava, S. Megavariate Data Analysis of Mass Spectrometric Proteomics Data Using Latent Variable Projection Method, Proteomics 1680-1686 (2004). 

Zhou, H. Ranish, J.A. Watts, J.D. Aebersold, R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat. Biotechnol. 2002, 20, 512-515. Qiu, Y. Sousa, E.A. Hewick, R.M. Wang, J.H. Acid-labile isotope-coded extractants a class of reagents for quantitative mass spectrometric analysis of complex protein mixtures. Anal. Chem. 2002, 74, 4969—4979. 

Protocols for mass spectrometric peptide analysis are common to modern and archaeological samples. The only significant difference in the analytical protocol used for archaeological samples is the need for careful sample extraction and preparation. In addition, the usefulness of archaeological proteomics requires the development of a database for archaeological peptide data, which will expand and increase over time but is currently relatively small. 

Besides sensitive methods for the analysis of proteins, bioinformatics is one of the key components of proteome research. This includes software to monitor and quantify the separation of complex samples, e.g., to analyze 2DE images. Web-based database search engines are available to compare experimentally measured peptide masses or sequence ions of protein digests with theoretical values of peptides derived from protein sequences. Websites for database searching with mass spectrometric data may be found at http //www.expasy.ch/tools, http //prospector.ucsf. edu/ and http //www.matrixscience.com. 

Mass spectrometric analysis of the glycosphingolipid-enriched microdomains of rat natural killer cells. Proteomics 5, 113-122. 

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. 

Hansen, K.C., Schmitt-Ulms, G., Chalkley, R.J., Hirsch, J., Baldwin, M.A., and Burlingame, A.L. (2003) Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography. Mol. Cell. Proteomics 2, 299-314. 

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