Abstract
One of the major goals of proteomic research is the identification of proteins, a goal that often requires various software tools and databases. These tools have to be able to handle large amounts of data, such as those generated by PMF (Peptide Mass Fingerprinting), a high throughput technique. A newly sequenced organism, Spirulina platensis, was recently used to generate an in silico database, and thus an in-house tool designed for compatibility with this database and its inputs (PMF) was constructed in the present study. With a probability based scoring function, this tool effectively ranked ambiguous protein identification results by using five criteria: score, number of matched peptides, % coverage, pI and molecular weight. As a result, the protein identification step of Spirulina proteomic studies can be achieved precisely. Moreover, a very useful function of this tool is its capability for batch processing, in which the system can handle proteinidentification searches of a hundred of proteins automatically, from a single user’s input. Therefore, the tool not only gives accurate protein identification results but also saves the user time in processing a large amount of data.
Highlights
The identification of differentially expressed proteins by employing experimental techniques and tools is a goal of proteomics
After protein isolation by various techniques, including two dimensional- gel electrophoresis (2D-PAGE), a protein of interest is subjected to protein identification by using mass spectrometry techniques coupled with bioinformatics
To manage the web interface, the input and output interfaces of this tool were created as Graphic User Interfaces (GUIs) in the HTML language employed in the Macromedia Dreamweaver MX program
Summary
The identification of differentially expressed proteins by employing experimental techniques and tools is a goal of proteomics. The ‘Hits’ results for each protein are shown, and Table 2 for photosystem II D1 (Synechocystis sp.PCC6803), and pyruvate kinase (E. coli K-12).
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