Mass spectrometry for proteomics

Hamler, R. L. Zhu, K. Buchanan, N. S. Kreunin, P. Kachman, M. T. Miller, F. R. Lubman, D. M. A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification. Proteomics 2004,4, 562-577. 

Chalmers MJ et al. Advances in mass spectrometry for proteome analysis. Curr Opin Biotechnol 2000 11 384—390. 

Shen, Y. R, Zhao, R., Belov, M. E., Conrads, T. R, Anderson, G. A., Tang, K. Q., Pasa-Tolic, L., Veenstra, T. D., Lipton, M. S., Udseth, H. R., and Smith, R. D., Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics. Analytical Chemistry 73(8), 1766-1775, 2001. 

Chalmers, M.J., Gaskell, S.J. (2000). Advances in mass spectrometry for proteome analysis. Curr. Opin. Biotechnol., 11(4), 384-390. 

Shen, Y. Zhao, R. Belov, M.E. Conrads, T.P. Anderson, G.A. Tang, K. Pasa-Tolic, L. Veenstra, T.D. Lipton, M.S. Udseth, H.R. Smith, R.D. Packed Capillary Reverse-Phase Liquid Chromatography with High-Performance Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Proteomics, Anal. Chem. 12>, Yl(>C-Vn5 (2001). 

Ahmed, F. E. 2009. Utility of mass spectrometry for proteome analysis Part II. Ion-activation methods, statistics, bioinformatics and annotation. Expert Rev. Proteomics 6(2) 171-97. 

Wang, Y., Fonslow, B.R., Wong, C.C., Nakorchevsky, A., and Yates, J.R., 3rd (2012) Improving the comprehensiveness and sensitivity of sheathless capillary electrophoresis-tandem mass spectrometry for proteomic analysis. Analytical Chemistry, 84, 8505. 

Vestal, M. Hayden, K. High Performance MALDI-TOF Mass Spectrometry for Proteomics. Int. J. Mass Spectrom. 2007,26S, 83-92. 

Molloy, M. P Donohoe, S. Brzezinski, E. E. Kilby, G. W. Stevenson, T. L Baker, J. D. Goodlett, D. R. Gage, D. A. Large-scale evaluation of quantitative reproducibility and proteome coverage using acid cleavable isotope coded affinity tag mass spectrometry for proteomic profiling. Proteomics 2005, 5, 1204-1208. 

Demirev, P. A. Lin, J. S. Pineda, F. J. Fenselau, C. Bioinformatics and mass spectrometry for microorganism identification Proteome-wide post-translational modifications and database search algorithms for characterization of intact H. Pylori. Anal. Chem. 2001, 73, 4566 573. 

DeSouza, L., Diehl, G., Rodrigues, M.J., Guo, J., Romaschin, A.D., Colgan, T.J., Siu, K.W. (2005). Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J. Proteome Res. 4, 377-386. 

Cargile, B.J., Bundy, J.L., Stephenson, JL., Jr. (2004). Potential for false positive identifications from large databases through tandem mass spectrometry. J. Proteome Res. 3, 1082-1085. 

General Strategy for Mass Spectrometry-Based Proteomics... 

MS instruments measure the mass-to-charge ratio (m/z) values of the smallest of molecules very accurately. In addition, the development of translated genomic databases and specialized software algorithms that rapidly search MS data against theoretical spectra of known or predicted proteins within databases is an important component that greatly facilitated the emergence of mass spectrometry-based proteomics as a key approach for large-scale proteomic analysis.15... 

The mass spectrometric information should ideally be sufficient to answer two questions about each sample what does it contain and how much In order to answer these questions appropriately a researcher has to face the three central problems of mass spectrometry based proteomic research (i) the design of the experiment to allow for detection of proteins that are present in low abundance in the biological system... 

Simpson, D. C., and Smith, R. D. (2005). Combining capillary electrophoresis with mass spectrometry for applications in proteomics. Electrophoresis 26, 1291-1305. 

Weissinger, E. M., Hertenstein, B., Mischak, H., and Ganser, A. (2005). Online coupling of capillary electrophoresis with mass spectrometry for the identification of biomarkers for clinical diagnosis. Expert Rev. Proteomics 2, 639—647. 

Zhang, S. Van Pelt, C. K. Chip-based nanoelectrospray mass spectrometry for protein characterization. Exp. Rev. Proteom. 2004, 1, 449-468. 

Mitulovic, G., Stingl, C., Smoluch, M., Swart, R., Chervet, J. P., Steinmacher, I., Gerner, C., and Mechtler, K., Automated, on-line two-dimensional nano liquid chromatography tandem mass spectrometry for rapid analysis of complex protein digests, Proteomics 4(9), 2545-2557, 2004. 

To facilitate our understanding of gene function, large-scale analyses of proteins are also necessary. Proteomics is currently divided into three main areas (1) mass spectrometry for characterization and identification of proteins (2) differential display proteomics for comparison of protein levels and (3) studies of protein-protein interaction by using the yeast two-hybrid system or phage display technology. 

Kim J, Kim SH, Lee SU et al. Proteome analysis of human liver tumor tissue by two-dimensional gel eleetrophoresis and matrix-assisted laser desorption/ionization-mass spectrometry for identification of disease-related proteins. Electrophoresis 2002 23 4142 156. 

Recent developments in instrument design have led to lower limits of detection, while new ion activation techniques and improved understanding of gas-phase ion chemistry have enhanced the capabilities of tandem mass spectrometry for peptide and protein structure elucidation. Future developments must address the understanding of protein-protein interactions and the characterization of the dynamic proteome (Chalmers and Gaskell 2000). 

Schmid, D. G., Grosche, P., Bandel, H., and Jung, G. (2000). FTICR-mass spectrometry for high-resolution analysis in combinatorial chemistry. Biotechnol. Bioeng. 71 149-161. Scigelova, M., and Makarov, A. (2006). Orbitrap mass analyzer—Overview and applications in proteomics. Proteomics 6 (Suppl. 2) 16-21. 

Reyzer, M. L., and Caprioli, R. M. (2005b). MALDI mass spectrometry for direct tissue analysis A new tool for biomarker discovery. J. Proteome Res. 4 1138-1142. 

The practice of protein analysis of whole proteomes relies on (i) two-dimensional gel electrophoresis for separation (ii) mass spectrometry for analysis and (iii) protein arrays for achieving massively parallel analysis. 

The detector in capillary electrophoresis is the main component in nanoanalyses. Many detectors can be used for this purpose but the mass spectrometer is the best one due to its wide ranges and low concentration detection capabilities. In the last few years, time-of-flight-mass spectrometry (TOF-MS) instruments have come onto the market and are available in many sizes, but small instruments are preferred in NCE. Bruker (Billerica, MA) has provided a micro-TOF-MS-LC (2x2x4 feet) system for nanoanalyses. Bruker also introduced a Q-q-FTMS (Fourier transform mass spectrometer) for proteomics called the APEX-QE. It offers fast, dual quadrupoles, which provides the first stages followed by FTMS for the highest mass accuracy. It can be coupled to NCE and controlled by Bmker s ProteinScape work flow and warehousing... 

Blackstock, W. 2000. Trends in automation and mass spectrometry for pro-teomics. In Proteomics A Trends Guide, Blackstock, W. R Mann, M., eds., Elsevier, New York, NY, 12-17. 

Liu N, Liu F, Xu B, Gao Y, Li X, Wei K, Zhang X, Yang S (2008) Establishment of imaging mass spectrometry for biological tissue and its application on the proteome analysis of micro-wave radiated hippocampus. Chin J Anal Chem 36(4) 421—425... 

Vegvari A, Fehniger T, Gustavsson L, Nilsson A, Andren P, Kenne K, Nilsson J, Laurell T, Marko-Varga G (2010) Essential tactics of tissue preparation and matrix nano-spotting for successful compound imaging mass spectrometry. J Proteomics 73 1270-1278. doi 10.1016/j. jprot.2010.02.021... 

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