Protein mixture analysis

Stephenson, J.L. McLuckey, S.A. Ion/ion proton transfer reactions for protein mixture analysis. AwaZ. Chem. 1996, 68, 4026 032. 

As will be discussed below, bromocolchicine is very reactive and can eventually bind covalently in a nonspecific way to a number of proteins other than tubulin. To assess the degree of specific labeling of tubulin in a complex protein mixture, analysis on sodium dodecyl sulfate (SDS)-polyacrylamide slab gels in one or two dimensions is a convenient method. 

For mixture.s the picture is different. Unless the mixture is to be examined by MS/MS methods, usually it will be necessary to separate it into its individual components. This separation is most often done by gas or liquid chromatography. In the latter, small quantities of emerging mixture components dissolved in elution solvent would be laborious to deal with if each component had to be first isolated by evaporation of solvent before its introduction into the mass spectrometer. In such circumstances, the direct introduction, removal of solvent, and ionization provided by electrospray is a boon and puts LC/MS on a level with GC/MS for mixture analysis. Further, GC is normally concerned with volatile, relatively low-molecular-weight compounds and is of little or no use for the many polar, water soluble, high-molecular-mass substances such as the peptides, proteins, carbohydrates, nucleotides, and similar substances found in biological systems. LC/MS with an electrospray interface is frequently used in biochemical research and medical analysis. 

Heilman, EJ., Wiksell, E., and Karlsson, B.-M. (1990). A new approach to micropreparative desalting exemplified by desalting a reduction/alkylation mixture, presenred ar Eighr International Conference on Methods in Protein Sequence Analysis, Kiruna, Sweden, July 1-6. 

For proteins, the most useful columns are those with pores of 100-500 A, as seen in Fig. 10.2, because most proteins elute on the linear portions of the calibration curves. Figure 10.5 illustrates an analysis of a protein mixture on SynChropak GPC100. Small peptides can be analyzed on the 50-A SynChro-pak GPC Peptide column with appropriate mobile-phase modifications. Many peptides have poor solubility in mobile phases standardly used for protein analysis, as discussed later in this chapter. 

H. Yamamoto, T. Manabe and T. Okuyama, Apparatus for coupled high-performance liquid chromatography and capillary electrophoresis in the analysis of complex protein mixtures , 7. Chromatogr. 515 659-666 (1990). 

Liquid samples might appear to be easier to prepare for LC analysis than solids, particularly if the compounds of interest are present in high concentration. In some cases this may be true and the first example given below requires virtually no sample preparation whatever. The second example, however, requires more involved treatment and when analyzing protein mixtures, the procedure can become very complex indeed involving extraction, centrifugation and fractional precipitation on reversed phases. In general, however, liquid samples become more difficult to prepare when the substances are present at very low concentrations. 

Dai, Y., Whittal R.M., and Li, L., Two-layer sample preparation a method for MALDI-MS analysis of complex peptide and protein mixtures, Anal. Chem., 71, 1087, 1999. 

Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999. 

D-polyacrylamide gel electrophoresis) maps of protein mixtures is discussed. 2D PAGE is considered the classical and principal tool for protein separation—prior to mass spectrometry—to achieve the main goal of proteomics, that is, a comprehensive identification and quantification of every protein present in a complex biological sample that would allow analysis of an entire intact proteome (Wilkins et al., 1997 Righetti et al., 2001 Hamdan and Righetti, 2005). 

The ability to resolve and characterize complicated protein mixtures by the combination of 2DLC and online mass spectrometry permits the combination of sample fractionation/simplification, top-down protein mass information, and bottom-up peptide level studies. In our lab, the simplified fractions generated by 2D(IEX-RP)LC are digested and analyzed using common peptide-level analysis approaches, including peptide mass fingerprinting (Henzel et al., 1993 Mann et al., 1993), matrix-assisted laser desorption/ionization (MALDI) QTOF MS/MS (Millea et al., 2006), and various capillary LC/MS/MS methodologies (e.g., Ducret et al., 1998). 

This chapter has presented several comprehensive 2DLC approaches combining a first-dimension IEX separation and a second-dimension RP separation for the analysis of complex protein mixtures typical in proteomics studies. Online ESI-TOF/MS detection provided sensitive detection and valuable qualitative information (MW) for proteins eluting from the MDLC system. Coordinated fraction collection and subsequent MS analysis of peptides produced by proteolysis of the fractions provided in-depth information on protein identification and a mechanism... 

TWO-DIMENSIONAL CAPILLARY ELECTROPHORESIS FOR THE COMPREHENSIVE ANALYSIS OF COMPLEX PROTEIN MIXTURES... 

As shown in the previous sections, identifying a small amount of a protein (in the order of tens of picomoles) represents a difficult problem for traditional methods of chemical analysis. The situation is even more complicated when a protein mixture of variable composition should be identified in a complex matrix containing dyes, oils, inorganic pigments, lime, etc. moreover, the analysed materials come often from the Middle Ages or even ancient times and the proteins in them could have undergone various modifications (e.g. oxidation, photodecomposition and microbial digestion) over the centuries. 

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. 

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. 

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