Protein database, analytical strategies

This strategy is highly successful for impurity identification (Kerns et al., 1995) during preclinical development. When information is stored within a comparative database, this approach is also highly effective for protein identification (Arnott et al., 1995). In these applications, the characteristic fragmentation corresponding to amino acid residues provides the searchable template for identification. This approach is particularly useful when identification studies are required for vast numbers of compounds or for samples that contain many analytes of interest. 

The study of protein structure, function, quantity, and interactions during maturation and progression of disease is referred to as proteomics. Analytical approaches that use a combination of two-dimensional (2-D) gel electrophoresis for protein separation and MS analysis for protein identification followed by database searches is a widely practiced proteomics strategy.The tryptic peptides extracted from gels are analyzed by MALDI-TOF MS and microcolunm or capillary LC tandem mass spectrometry (MS/MS) techniques. Typically, the MALDI-TOF MS techniques are used to quickly identify peptide fragments and confirm the presence of known proteins. Nano-scale capillary LC/MS/MS techniques (using 50-100 pm diameter columns, operating at flow rates of 20-500 nL/min) are... 

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