Application of Relative Warp Analysis to the Evaluation of Two-Dimensional Gels in Proteomics:  Studying Isoelectric Point and Relative Molecular Mass Variation

We propose a geometric-morphometrics method (relative warp analysis) to be used in proteomic comparisons. This approach was applied to a dataset from a comparison between 5 controls and 5 patients with colorectal cancer disease published elsewhere. The spots in the 2-D maps were used as landmarks in...

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Bibliographic Details
Published in:Journal of proteome research 2005-07, Vol.4 (4), p.1318-1323
Main Authors: Rodríguez-Piñeiro, Ana M, Carvajal-Rodríguez, Antonio, Rolán-Alvarez, Emilio, Rodríguez-Berrocal, Francisco J, Martínez-Fernández, Mónica, Páez de la Cadena, María
Format: Article
Language:English
Subjects:
Electrophoresis, Gel, Two-Dimensional
Humans
Image Processing, Computer-Assisted - methods
Isoelectric Point
Molecular Weight
Neoplasm Proteins - analysis
Neoplasms - diagnosis
Neoplasms - metabolism
Proteome - analysis
Proteomics - methods
Reproducibility of Results
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Summary:We propose a geometric-morphometrics method (relative warp analysis) to be used in proteomic comparisons. This approach was applied to a dataset from a comparison between 5 controls and 5 patients with colorectal cancer disease published elsewhere. The spots in the 2-D maps were used as landmarks in a morphometric study, and the differences in shape (spot distribution) among them were obtained. The shape variables were used to compare controls and patients. These components mostly ignore random or experimental effects affecting all the proteins in any of the two dimensions studied. Furthermore, the method allows the researcher to find those proteins which contributed the most to the local shape component detected. Applying this approach, we detected variations in the position (isoelectric point and/or relative molecular mass) of some spots that may reflect differences in the amino acidic sequence or post-translational modifications. Keywords: two-dimensional gel electrophoresis • geometric-morphometrics • relative warps • spot position • isoelectric point • relative molecular mass
ISSN:1535-3893
1535-3907
DOI:10.1021/pr0500307