Protein mass spectrometric identification

Toews J, Rogalski JC, Clark TJ, et al. Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions. Anal. Chim. Acta. 2008 618 168-183. 

Gharahdaghi, F., Weinberg, C. R., Meagher, D. A., and Imai, B. S. (1999) Mass spectrometric identification of proteins from silver-stained polyacrylamide gel a method for the removal of silver ions to enhance sensitivity. Electrophoresis 20, 601-605. 

The most widely used mass spectrometric identification procedure is MALDI-Tof analysis of the entire peptide mixture. Gas-phase matrix interaction with peptide ions in MALDI-Tof results in singly charged ions, giving a mass profile that is highly characteristic of the protein from which the peptides are derived. These peptide masses (actually protonated peptide molecular ions, MH+) can be used to search databases (either protein or nucleic acid databases) to identify the proteins. The two most important factors in successfully identifying proteins by this approach are the number of matching peptide masses and the accuracy of the peptide mass determination. 

G Li, M Waltham, NL Anderson, E Unsworth, A Treston, IN Weinstein. Rapid mass spectrometric identification of proteins from two-dimensional polyacrylamide gels after in gel proteolytic digestion. Electrophoresis 18 391-402, 1997. 

Proteomics is a modem parallel approach for investigating protein expression in experimental systems. In pharmaceutical research, this methodology is used to accelerate the discovery of novel drug targets and biomarkers. Among the several possible techniques for the study of proteomes, the combination of two-dimensional polyacrylamide electrophoresis with mass spectrometric identification of the separated proteins has gained wide popularity. This technique involves the analysis of vast numbers of small gel spots that are excised from two-dimensional protein separation... 

Gevaert, K., Goethals, M., Martens, L., Van Daimne, J., Staes, A., Thomas, G.R. and Vandekerckhove, J. (2003) Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted V-terminal peptides. Nat. Biotechnol. 21, 566-569. 

Rais, I., Karas, M. and Schagger, H. (2004) Two-dimensional electrophoresis for the isolation of integral membrane proteins and mass spectrometric identification. Proteomics 4, 2567-2571. 

Mass Spectrometric Identification of Interacting Proteins. The preparation of proteins obtained after TAP is introduced into a spectrometer, and the different proteins are identified. In such an analysis, a sample of protein affinity purified using the epitope tag and the one without the epitope tag is labeled with stable isotopes and then compared for the relative abundance of different peaks in the two samples to determine the interacting proteins in a particular preparation. Thus, this is essentially a quantitative ICAT mass spectrometry described in Chapter 4. In case the proteins are purified over a DNA column without the use of an epitope tag, it is compared with a sample that cannot bind with DNA in the matrix. The samples are labeled with stable isotopes. The interacting proteins are identified by their relative abundance. 

Ohtsu, L, Nakanisi, T, Furuta, M., Ando, E., and Nishimura, O., Direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometric identification of proteins on membrane detected by Western blotting and lectin blotting, Journal ofProteome Research, 4, 1391-1396, 2005. 

Jensen, O.N., Larsen, M.R., and Roepstorff P. (1998) Mass spectrometric identification and microcharacterization of proteins from electrophoretic gels strategies and applications. Proteins Struct. Funct. Genet, 33 (Suppl. 2), 74-89. Shevchenko, A., Jensen, O.N., Podtelejnikov, A.V., SagUocco, F Wilm,... 

Thevis, M., Loo, J.A., Loo, R.R., and Schanzer, W. (2007) Recoimnended criteria for the mass spectrometric identification of target peptides and proteins (<8kDa) in sports drug testing. Rapid Communications in Mass Spectrometry, 21,297-304. 

Bemdt, P., Hobohm, U., and Langen, H. (1999). Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints. Electrophoresis 20, 3521-3526. 

Wang, Z. Dunlop, K. Long, S. R. Li, L. Mass spectrometric methods for generation of protein mass database used for bacterial identification. Anal. Chem. 2002, 74,3174-3182. 

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. 

Merkel, D., et al., Proteomic study of human bronchoalveolar lavage fluids from smokers with chronic obstructive pulmonary disease by combining surface-enhanced laser desorp-tion/ionization-mass spectrometry profiling with mass spectrometric protein identification, Proteomics. 5, 11, 2972, 2005. 

J. Eriksson, B. T. Chait, and D. Fenyo. A Statistical Basis for Testing the Significance of Mass Spectrometric Protein Identification Results. Anal Chem., 12, no. 5 (2000) 999-1005. 

W. Zhang and B. T. Chait. ProFound An Expert System for Protein Identification Using Mass Spectrometric Peptide Mapping Information. Anal. Chem., 72, no. 11 (2000) 2482-2489. 

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