Affinity-proteomics

Macht, M., Marquardt, A., Deininger, S.O. et al. (2004) Affinity-proteomics direct protein identification from biological material using mass spectrometric epitope mapping. Anal. Bioanal. Chem., 378, 1102-11. 

Tian, X., Cecal, R., Mezo, G., Manea, M., Stefanescu, R., McLaurin, J., St George-Hyslop, R, Hudecz, F. and Przybylski, M. (2004) New amyloid-derived vaccine lead stmctures against Alzheimer s disease discovered by affinity proteomics and high resolution mass spectrometry. In Innovation and Perspectives in Antibody and Peptide Vaccine Development, R. Epton, ed. (Kingswinford, UK Mayflower Worldwide Ltd), p. 79. 

Ayoglu, B., A. Chaouch, H. Lochmuller, L. Politano, E. Bertini, P. Spitali, M. Hiller, E. H. Niks, F. Gualandi, F. Ponten, K. Bushby, A. Aartsma-Rus, E. Schwartz, Y. Le Priol, V. Straub, M. Uhlen, S. Cirak, P. A. t Hoen, F. Muntoni, A. Ferlini, J. M. Schwenk, P. Nilsson, and C. Al-Khalili Szigyarto (2014). Affinity proteomics within rare diseases a BIO-NMD study for blood biomarkers of muscular dystrophies. EMBO Mol Med 6(7) 918-936. 

Figure 4.4 Example of linker SAR and minimal small-molecule functionalization for affinity proteomics of selective modulators of Wnt signaling in colorectal cancer cells [17].

Figure 2.2. Fractionation of protein extracts before 2D gel electrophoresis. Crude lysates can be fractionated by affinity purification or by a number of chromatographic techniques. In addition, organelles or other cellular structures can be purified and lysates from these organelles can be fractionated or separated directly on 2D gels. By repeating this procedure using a number of conditions it may be possible to visualize a large fraction of a cell s proteome.

Another means of moving beyond pure protein preparations to high-throughput characterization of proteomes is to enrich for phosphopeptides from complex mixtures by metal affinity chromatography (Andersson and Porath, 1986). Using this method, protein mixtures are proteolyzed to create peptides and phosphorylated peptides are enriched by metal affinity chromatography and subsequently identified by mass spectrometry. This method is limited, however, because in many cases phosphopeptides absorb poorly or nonphosphorylated peptides absorb nonspecifically to the metal affinity resins (Ahn and Resing, 2001). 

Regnier, F. E. Riggs, L. Zhang, R. Xiong, L. Liu, P. Chakraborty A. Seeley E. Sioma, C. Thompson, R. A. Comparative proteomics based on stable isotope labeling and affinity selection. J. Mass. Spectrom. 2002,37,133-145. 

FIGURE 9.1 Liquid chromatography workflow strategy options in proteomics. (a) bottom-up approach (b) top-down approach (c) selective sample cleanup directly combined with chromatographic separation (d) peptide capture with affinity restricted access material. 

Graumann, J., Dunipace, L.A., Seol, J.H., McDonald, W.H., Yates, J.R., 3rd Wold, B.J., Deshaies, RJ. (2004). Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast. Mol. Cell. Proteomics 3, 226-237. 

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. 

Geng, M., Zhang, X., Bina, M., Regnier, F. (2001). Proteomics of glycoproteins based on affinity selection of glycopeptides from tryptic digests. J. Chromatogr. B 752, 293-306. 

Lopez MF et al. High-throughput profiling of the mitochondrial proteome using affinity fractionation and automation. Electrophoresis 2000 21 3427-3440. Reinheckel T et al. Adaptation of protein carbonyl detection to the requirements of proteome analysis demonstrated for hypoxia/reoxygenation in isolated rat liver mitochondria. Arch Biochem Biophys 2000 376 59-65. 

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. 

Fetsch PA, Simone NL, Bryant-Greenwood PK, et al. Proteomic evaluation of archival cytologic material using SELDI affinity mass spectrometry potential for diagnostic applications. Am. J. Clin. Pathol. 2002 118 870-876. 

Guerrero C, Tagwerker C, Kaiser P, et al. An integrated mass spectrometry-based proteomic approach quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol. Cell. Proteomics. 2006 5 366-378. 

The preparation of particles or surfaces that are able to capture specifically a fraction of he proteome using metal affinity separations makes possible analysis of distinct protein... 

Fauq, A.H., Kache, R., Khan, M.A., and Vega, I.E. (2006) Synthesis of acid-cleavable light isotope-coded affinity tags (ICAT-L) for potential use in proteomic expression profiling analysis. Bioconjugate Cbem. 17, 248-254. 

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. 

Lee, S., Young, N.L., Whetstone, P.A., Cheal, S.M., Benner, W.H., Lebrilla, C.B., and Meares, C.F. (2006) A method to site-specifically identify and quantitate carbonyl end products of protein oxidation using oxidation-dependent element coded affinity tags (O-ECAT) and nanoLiquid chromatography Fourier transform mass spectrometry./. Proteome Res. 5(3), 539-547. 

Li, J., Steen, H., and Gygi, S.P. (2003) Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents. The yeast salinity stress response. Mol. Cell. Proteomics 2, 1198-1204. 

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