Probability-Based Scoring Function as a Software Tool Used in the Genome-Based Identification of Proteins from Spirulina platensis

Wimada, Thammasorn; Korakot, Eadjongdee; Apiradee, Hongsthong; Kriengkrai, Porkaew; Supapon, Cheevadhanarak

Probability-Based Scoring Function as a Software Tool Used in the Genome-Based Identification of Proteins from Spirulina platensis

Thammasorn Wimada¹, Eadjongdee Korakot¹, Hongsthong Apiradee^{*, 2}, Porkaew Kriengkrai¹, Cheevadhanarak Supapon³

¹ School of Information Technology, King Mongkut's University of Technology Thonburi, 126 Pracha-U-Thit Rd., Bangmod, Thungkru, Bangkok 10140, Thailand

² BEC Unit, KMUTT-Bangkhuntien, 83 Moo 8, Thakham, Bangkhuntien, Bangkok 10150, Thailand

³ School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand

Article Information

Identifiers and Pagination:

Year: 2009
Volume: 3
First Page: 59
Last Page: 68
Publisher ID: TOBIOIJ-3-59
DOI: 10.2174/1875036200903010059

Article History:

Received Date: 25/06/2009
Revision Received Date: 14/08/2009
Acceptance Date: 21/08/2009
Electronic publication date: 01/10/2009
Collection year: 2009

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© 2009 Wimada et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

^* Address correspondence to this author at the BEC Unit, KMUTT, 83 Moo8, Thakham, Bangkhuntien, Bangkok 10150, Thailand; Tel: 662-470- 7509; Fax: 662-452-3455; E-mails: apiradee@biotec.or.th, apiradee@pdti.kmutt.ac.th

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.

Keywords: Peptide Mass Fingerprinting (PMF), S. platensis, 2D-DIGE, Protein isoelectric points (pI), Bisection method and Probability-based scoring function.

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RESEARCH ARTICLE

Probability-Based Scoring Function as a Software Tool Used in the Genome-Based Identification of Proteins from Spirulina platensis

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