Protein Identification Using Bioinformatics Tools

Bioinformatics is also concerned by the huge amount of data generated experimentally by the wet-lab, as well as the data generated by its tools outputs. In this case, a laboratory management systems (LIMS) must be precisely designed for each specific need. 

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The most common implementation of proteomic analysis involves protein separation two-dimensional gel electrophoresis (2DGE), quantification of proteins with analytical methods for their identification in mass spectrometer (MS), and at the very least data integration and analysis using bioinformatic tools. 

These protein attributes are then submitted to a database search. This search identifies a protein by looking at the best match between experimental data and data obtained by in-silico processing and digestion of a protein sequence database. The identification and characterization procedures using bioinformatics tools will be the topic of Section 4.4. 

Bioinformatics tools involving computer-based statistical analyses are essential for data management and analysis. When a complex biological sample containing thousands of different proteins is analyzed by multifaceted approaches, such as multidimensional protein identification technology, the identification of the proteins in the mixture is extremely complicated. Even multiple peptide identification methods, such as using both MS and... 

Some bioinformatics software tools for proteomics combine data analysis, statistics and artificial intelligence methods to manage MS data, to identify proteins and to update databases. In this section, specific tools used to identify proteins are reviewed. They use lists of peptide mass values from MS or MS/MS as input, and they may also combine this information with amino acid sequence tag information or amino acid composition to enhance the identification of proteins. Figure 6 shows a simplified flow chart of sample preparation and MS data collection. It also shows the techniques and tools for protein identification described in this section. 

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