Biology Reference
In-Depth Information
Chapter 5
Standardization of Data Processing and Statistical
Analysis in Comparative Plant Proteomics Experiment
Luis Valledor, M. Cristina Romero-RodrÃguez, and Jesus V. Jorrin-Novo
Abstract
Two-dimensional gel electrophoresis remains the most widely used technique for protein separation in
plant proteomics experiments. Despite the continuous technical advances and improvements in current
2-DE protocols, an adequate and correct experimental design and statistical analysis of the data tend to be
ignored or not properly documented in current literature. Both proper experimental design and appropriate
statistical analysis are requested in order to confidently discuss our results and to conclude from experi-
mental data.
In this chapter, we describe a model procedure for a correct experimental design and a complete
statistical analysis of proteomic dataset. Our model procedure covers all of the steps in data mining and
processing, starting with the data preprocessing (transformation, missing value imputation, definition of
outliers) and univariate statistics (parametric and nonparametric tests), and finishing with multivariate
statistics (clustering, heat-mapping, PCA, ICA, PLS-DA).
Key words
2-DE-based proteomics, Experimental design, Data mining, Univariate statistics,
Multivariate statistics, Systems biology
1
Introduction
Comparative or quantitative proteomics is the most utilized subarea
of proteomics [
1
,
2
]. It aims at establishing differences in protein
profiles between two samples from different individuals or from
distinct treatments, defined both from a quantitative and qualita-
tive point of view. In most of the cases the final objective of these
methodologies is to differentially identify abundant protein species
in order to explain the biological characteristics of each system.
Two-DE continues, by far, as the most frequently used tool in
plant proteomics among the current proteomic platforms, while
gel-free LC-MS methods are still used in a minimum percentage of
the papers published. Even so, and despite the continuous technical
