Author: Maurer, Martin H.

Source: Current Bioinformatics, Volume 1, Number 2, May 2006 , pp. 255-262(8)

Publisher: Bentham Science Publishers

Abstract:

Two-dimensional gel electrophoresis in combination with mass spectrometry constitutes the backbone of proteomic analysis. With the availability of powerful software tools addressing the specific needs for analyzing twodimensional gels, several typical procedures have been elaborated. In the first part of this review, we will describe and discuss the procedure of analyzing two-dimensional electrophoretic gels consisting of (i) digitizing the gels, (ii) detecting and separating individual spots, (iii) background subtraction, (iv) creating a reference gel and (v) matching the spots to the reference gel, (vi) modifying the reference gel, (vii) normalizing the gel measurements for comparison, and (viii) calibrating for isoelectric point and molecular weight markers. In the next step, (ix) a database containing the measurement results is constructed and (x) data are compared by statistical and bioinformatic means. We compare the software currently available for performing these tasks in the light of recent benchmarking and standardization efforts. We also comment on the statistical means provided in the programs including t-test statistics, ANOVA, and additional software for comparing expression patterns in large gel datasets, including hierarchical clustering algorithms and selforganizing maps (SOMs).

Keywords: Proteomics; gel electrophoresis; two-dimensional; bioinformatics; image analysis; hierarchical clustering; 2D software

Document Type: Research article

DOI: http://dx.doi.org/10.2174/157489306777011969

Affiliations: 1: Dept. of Physiology and Pathophysiology, University of Heidelberg, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany.

Publication date: 2006-05-01

More about this publication?

• Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a wide range of the integration of biology with computer and information science.
  
  The journal focuses on reviews on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.
  
  Current Bioinformatics is an essential journal for all academic and industrial researchers who want expert knowledge on all major advances in bioinformatics.

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