Biology Reference
In-Depth Information
Chapter 20
Arabidopsis Proteomics: A Simple and Standardizable
Workflow for Quantitative Proteome Characterization
Anja Rödiger, Birgit Agne, Katja Baerenfaller, and Sacha Baginsky
Abstract
Arabidopsis is the model plant of choice for large-scale proteome analyses, because its genome is well
annotated, essentially free of sequencing errors, and relatively small with little redundancy. Furthermore,
most Arabidopsis organs are susceptible to standard protein solubilization protocols making protein
extraction relatively simple. Many different facets of functional plant proteomics were established with
Arabidopsis such as mapping the subcellular proteomes of organelles, proteo-genomic peptide mapping,
and numerous studies on the dynamic changes in protein modification and protein abundances. As most
standard proteomics technologies are now routinely applied, research interest is increasingly shifting
towards the reverse genetic characterization of gene function at the proteome level, i.e., by profiling the
quantitative proteome of wild type in comparison with mutant plant tissue. We report here a simple, stan-
dardizable protocol for the large-scale comparative quantitative proteome characterization of different
Arabidopsis organs based on normalized spectral counting and suggest a statistical framework for data
interpretation. Based on existing organellar proteome maps, proteins can be assigned to organelles, thus
allowing the identification of organelle-specific responses.
Key words
Arabidopsis proteomics, Quantitative plant proteomics, Spectral counting
Abbreviations
nSpC
Normalized spectral counting
MTP
Measured spectra of tryptic peptides
TTP
Theoretical tryptic peptides
1
Introduction
The systematic identification, quantification, and characterization
of proteins is an important strategy to characterize the effect of a
gene defect at large scale. It is expected that comparative quantita-
tive proteome analyses between wild-type and mutant plants will
provide information about the consequences of a gene defect that
reflects the functional footprint of a gene much closer than most
