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 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.
Rodríguez-Piñeiro
Ana M
AM
Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Campus Universitario, 36310 Vigo, Spain.
Carvajal-Rodríguez
Antonio
A
Rolán-Alvarez
Emilio
E
Rodríguez-Berrocal
Francisco J
FJ
Martínez-Fernández
Mónica
M
Páez de la Cadena
María
M
D015180:Electrophoresis, Gel, Two-Dimensional; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D007526:Isoelectric Point; D008970:Molecular Weight; D009363:Neoplasm Proteins / Q000032:analysis; D009369:Neoplasms / Q000175:diagnosis / Q000378:metabolism; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results
D009363:Neoplasm Proteins; D020543:Proteome