Tandem mass tags

Thompson, A., Schafer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., and Hamon, C. (2003) Tandem mass tags A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chern. 75(8), 1895-1904. 

The major advantage of the tandem mass spectrometry approach compared to MALDI peptide fingerprinting, is that the sequence information obtained from the peptides is more specific for the identification of a protein than simply determining the mass of the peptides. This permits a search of expressed sequence tag nucleotide databases to discover new human genes based upon identification of the protein. This is a useful approach because, by definition, the genes identified actually express a protein. 

Figure 2.7. Identification ofphosphoproteins by site-specific chemical modification. A. Method of Zhou et al. (2001) involves trypsin digest of complex protein mixture followed by addition of sulfhydryl groups specifically to phosphopeptides. The sulfhydryl group allows capture of the peptide on a bead. Elution of the peptides restores the phosphate and the resulting phosphopeptide is analyzed by tandem mass spectrometry. B. Method of creates a biotin tag in place of the phosphate group. The biotin tag is used for subsequent affinity purification. The purified proteins are proteolyzed and identified by mass spectrometry.

Mortz, E. O Connor, P. B. Roepstorff, P. Kelleher,N. L. Wood,T. D. McLafferty, F. W. Mann, M. Sequence tag identification of intact proteins by matching tandem mass spectral data against sequence data bases. Proc Nat. Acad. Sci. USA 1996, 93, 8264-8267. 

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. 

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. 

Thompson, A., Prescott, M., Chelebi, N., Smith, J., Brown, T., and Schmidt, G. (2007) Electrospray ionisation-cleavable tandem nucleic acid mass tag-peptide nucleic acid conjugates Synthesis and applications to quantitative genomic analysis using electrospray ionisation-MS/MS. Nucleic Acids Res. 35(4), e28. 

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. 

The second approach is the tandem mass spectrometric method (Wilm et ah, 1996 Link et ah, 1999 Yates, 2000). This method relies on fragmentation of individual peptides in the tryptic peptide mixture to gain sequence information. Its main advantage is that sequence information derived from several peptides is much more specific for the identification of a protein than a list of peptide masses. The sequence data can be used to search not only protein sequence databases but also nucleotide databases such as expressed sequence tag (EST) databases and, more recently, even... 

Fig. 17.9. Schematic diagram of MuDPIT proteomics (adapted from Yates, 1998). Protein mixtures of interest are cleaved via proteolytic activity and separated via a series of liquid chromatography separations. Identification of the proteins present relies on sequence tags produced from tandem mass spectrometry. Even low-abundance proteins should be represented at least on one occasion.

Lane SJ, Pipe A, Unambiguous bead decoding by microelectrospray capillary electrochromatography tandem mass spectrometry of dansylated secondary amine tags from encoded combinatorial organic synthesis, Rapid Common. Mass Spectrom., 12 667-674, 1998. 

Yan W, Lee H, Deutsch EW, Lazaro CA, Tang W, Chen E, et al. A dataset of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. Mol Cell Proteomics 2004 3(10) 1039-1041. 

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