Tandem mass spectrometry Proteomics

Qian, W.J., Jacobs, J.M., Camp, D.G., 2nd, Monroe, M.E., Moore, R.J., Gritsenko, M.A., Calvano, S.E., Lowry, S.F.,Xiao, W.,Moldawer, L.L., Davis, R.W., Tompkins, R.G., Smith, R.D. (2005a). Comparative proteome analyses of human plasma following in vivo lipo-polysaccharide administration using multidimensional separations coupled with tandem mass spectrometry. Proteomics 5, 572-584. 

Vitali, B., Wasinger, V., Brigidi, P., Guilhaus, M. (2005). A proteomic view of Bifidobacterium infantis generated by multi-dimensional chromatography coupled with tandem mass spectrometry. Proteomics 5, 1859-1867. 

Mamone, G., Addeo, F., Chianese, L., Di Luccia, A., De Martino, A., Nappo, A., Formisano, A., De Vivo, P., and Ferranti, P. (2005), Characterization of wheat gliadin proteins by combined two-dimensional gel electrophoresis and tandem mass spectrometry, Proteomics, 5(11), 2859-2865. 

Li, N., Shaw, A.R., Zhang, N.,Mak,A. andLi, L.(2004)Lipidraftproteomics analysis of in-solution digest of sodium dodecyl sulfate-solubilized lipid raft proteins by liquid chromatography-matrix-assisted laser desorption/ionization tandem mass spectrometry. Proteomics 4, 3156-3166. 

Huq M D, Khan S A, Park S W, et al. (2005). Mapping of phosphorylation sites of nuclear corepressor receptor interacting protein 140 by liquid chromatography-tandem mass spectrometry. Proteomics. 5 2157-2166. 

ID-LC-MS Shotgun Tandem Mass Spectrometry Proteomic Analysis 1494... 

Cho, H., Smalley, D. M., Theodorescu, D Ley, K., and Lee, J. K. (2007). Statistical identification of differentially labeled peptides from liquid chromatography tandem mass spectrometry. Proteomics, 7(20) 3681-3692. 

Meany, D.L. Xie, H. Thompson, L.V. Arriaga, E.A. Griffin, T.J. Identification of carbonylated proteins from enriched rat skeletal muscle mitochondria using affinity chromatography-stable isotope labeling and tandem mass spectrometry. Proteomics 2007, 7, 1150-1163. 

Purvine S, et al. Spectral quality assessment for high-throughput tandem mass spectrometry proteomics. OMICS A J Integrative Biol 2004 8 255-265. 

Lee, Y. H., Kim, M. S., Choie, W. S., Min, H. K., Lee, S. W. (2004) Hi y informative proteome analysis by combining improved N-terminal sulfonation for de novo peptide sequencing and online capillary reverse-phase liquid chromatography/tandem mass spectrometry. Proteomics, 4, 1684-1694. 

In E. Coli bacterial lysates, the proteome (i.e., the full array of proteins produced) was analyzed by isoelectric focusing and mass spectrometry.97 A comparison of capillary electrophoretic separation and slab gel separation of a recombinant monoclonal antibody demonstrated that the precision, robustness, speed, and ease-of-use of CE were superior.98 Seventy-five proteins from the yeast ribosome were analyzed and identified by capillary electrophoresis coupled with MS/MS tandem mass spectrometry.99 Heavy-chain C-terminal variants of the anti-tumor necrosis factor antibody DE7 have been separated on capillary isoelectric focusing.100 Isoforms differing by about 0.1 pi units represented antibodies with 0,1 or 2 C-terminal lysines. 

Dworzanski, J. R Snyder, A. P. Chen, R. Zhang, H. Wishart, D. Li, L. Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring. Anal. Chem. 2004,76,2355-2366. 

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. 

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. 

Gaucher, S.P., Taylor, S.W., Fahy, E., Zhang, B., Wamock, D.E., Ghosh, S.S., Gibson, B.W. (2004). Expanded coverage of the human heart mitochondrial proteome using multidimensional liquid chromatography coupled with tandem mass spectrometry. J. Proteome Res. 3, 495-505. 

Mawuenyega, K.G., Kaji, H., Yamuchi, Y., Shinkawa, T., Saito, H., Taoka, M., Takahashi, N., Isobe, T. (2003). Large-scale identification of Caenorhabditis elegans proteins by multidimensional liquid chromatography—tandem mass spectrometry. J. Proteome Res. 2, 23-35. 

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. 

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. 

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. 

Zhang, H., Yan, W., and Aebersold, R. (2004) Chemical probes and tandem mass spectrometry A strategy for the quantitative analysis of proteomes and subproteomes. Curr. Opin. Chem. Biol. 8, 66-75. 

TOF analyzers are especially compatible with MALDI ion sources and hence are frequently coupled in aMALDI-TOF configuration. Nevertheless, many commercial mass spectrometers combine ESI with TOF with great success. For proteomics applications, the quadrupole TOF (QqTOF) hybrid instruments with their superior mass accuracy, mass range, and mass resolution are of much greater utility than simple TOF instruments.21,22 Moreover, TOF instruments feature high sensitivity because they can generate full scan data without the necessity for scanning that causes ion loss and decreased sensitivity. Linear mode TOF instruments cannot perform tandem mass spectrometry. This problem is addressed by hybrid instruments that incorporate analyzers with mass selective capability (e.g., QqTOF) in front of a TOF instrument. 

M. Pelzing and C. NeusiiB. Separation Techniques Hyphenated to Electrospray-Tandem Mass Spectrometry in Proteomics Capillary Electrophoresis versus Nanoliquid Chromatography. Electrophoresis, 26(2005) 2717-2728. 

J. Peng, et al., 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, no. 1 (2003) 43-50. 

Peptide and protein sequencing and its importance in the proteomics field were discussed in Section 2.2.3. The following gives a brief description of the mass spectrometry methods used to achieve sequencing. First, to produce protein or oligonucleotide structural/sequence information by mass spectro-metric techniques, one needs to use tandem mass spectrometry (MS-MS). In this technique, a sample is first fragmented and analyzed in one mass spec-... 

Powell, M. J., Sutton, J. N., Del Castillo, C. E., and Timperman, A. I., Marine proteomics Generation of sequence tags for dissolved proteins in seawater using tandem mass spectrometry. Marine Chemistry 95(3 ), 183-198, 2005. 

Ishihama, Y., Proteomic LC-MS systems using nanoscale liquid chromatography with tandem mass spectrometry. Journal of Chromatography A 1067(1-2), 73-83, 2005. 

Madera, M., Mechref, Y, Klouckova, I., and Novotny, M. V., Semiautomated high-sensitivity profiling of human blood serum glycoproteins through lectin preconcentration and multidimensional chromatography/tandem mass spectrometry. Journal of Proteome Research 5(9), 2348-2363, 2006. 

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. 

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