Databases interrogation

Database Interrogation (Profound, Sequest) Protein Identification Post-translational Modification Characterization... 

Pairwise comparison of two sequences is a fundamental process in sequence analysis. It defines the concepts of sequence identity, similarity, and homology as applied to two proteins, DNA or RNA sequences. Database interrogation can take the form of text queries or sequence similarity searches. Typically, the user employs a query sequence to conduct sequence similarity search so that the relationships between the query sequence (probe) and another sequence (target) can be quantified and their similarity assessed. 

Liska, A.J. and Shevchenko, A. (2003) Combining mass spectrometry with database interrogation strategies in proteomics. Trends Anal. Chem., 22, 291-8. 

Chemindex plus. This database contains 8000 pharmaceutical ingredients linked to 300,000 preparations. Chemindex plus [66] can be interrogated at the national or international level. It covers compounds available in 55 countries recording their brand name, local manufacturer, launch date, therapeutic class, and base forms. This product is commercially available from IMS HEALTH Global Services. 

Several algorithms are available for the analysis of MS/MS spectra including SEQUEST, MASCOT, and X Tandem among others. Note that additional secondary quality control of assessment of MS/MS data has recently been implemented to assess identification probabilities and false positivity rates. The MS/MS spectra from an experiment can be interrogated against a concatenated forward and reverse database and an assessment of the intrinsic error rate of the data set can be made. Other approaches for secondary analysis of matching scores for peptide sequencing data include XCorr score normalization routines that are independent of peptide and database size.33... 

Next, custom software is used to interrogate the deconvoluted data set to identify the protein s mass and the intensity of the peak, determine any potential modification above a user-defined intensity threshold and, if there is a hit, calculate the mass and the relative conjugation of the fragment. In fact, the percent conjugation is used as a measure of relative affinities of the fragment hits. Since the library is mass encoded (all compounds in a well have a unique mass), the calculated mass of any hits are queried into a database to identify their structures. 

Using the isoTOP-ABPP method, the soluble proteome of the breast cancer cell line MCF7 was interrogated and, of the 800 probe-labeled cysteines, 10% were found to be hyper-reactive (/ io i < 2). A database search further revealed that hyper-reactive cysteines were over-represented in functional residues (active site... 

For pharmaceutical applications, the generation and sequencing of cDNA libraries from key tissues, and the assembly, curation and interrogation of the resulting enormous sequence databases, have proved particularly informative. 

It is now relatively easy to use sequence analysis software to interrogate databases for similarity of a new, or query sequence to existing sequences in the database, and to assess the degree of similarity with the subject sequences identified. The process of comparison involves the use of algorithms, which are dearly defined rules or criteria, which the comparison programme executes. The algorithms used depend on the nature of the problem and the type of comparison attempted. 

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