Protein analysis tools

Besides sensitive methods for the analysis of proteins, bioinformatics is one of the key components of proteome research. This includes software to monitor and quantify the separation of complex samples, e.g., to analyze 2DE images. Web-based database search engines are available to compare experimentally measured peptide masses or sequence ions of protein digests with theoretical values of peptides derived from protein sequences. Websites for database searching with mass spectrometric data may be found at http //www.expasy.ch/tools, http //prospector.ucsf. edu/ and http //www.matrixscience.com. 

Oda RP, Clark R, Katzman JA, Landers JP (1997) Capillary electrophoresis as a clinical tool for the analysis of protein in serum and other body fluids. Electrophoresis 18 1715-1723. 

Reversed-phase (rp-) or hydrophobic (HIC) HPLC is an excellent tool for analysis of proteins and peptides. Especially phenyl media, e.g., TosoHaas TSK-Gel Phenyl-5PW-RP, fit well... 

The use of fluorine has become well established in the analysis of protein structure and function, for example, in tools such as F NMR (nuclear magnetic... 

Technically, the AM1/DFT correction is now implemented as a combination of the structure analysis tool COSMO/yze developed for COSMO/rag and the MOPAC2002 program [59]. COSMO/y-ze analyses the bond types of a new protein and writes an input file for MOPAC, which contains all the correction charges for atoms and bond centers. By a small modification, MOPAC2002 is now able to read these AM1/DFT correction charges and to add the corresponding corrections to the electrostatic potential on the COSMO surface at the end of a MOPAC/COSMO calculation. In a final COSMO call, the improved potential is converted into updated COSMO charges and a COSMO file with quality closer to BP-SVP quality is written. 

In a study of the Qa-2-expression regulation by the transporter associated with antigen processing (TAP) protein, Ke and Warner [14] reported the monitoring of preimplantation embryos from TAP-1 knockout and normal mice by IPCR and RT-PCR. IPCR was carried out as described by McElhinny et al. [17]. Again, IPCR proved its potential as a valuable tool for the analysis of protein expression on the cell surface from small numbers (2-20) of one-cell and two-cell embryos, as well as blastocystes. 

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