title: Proteome analysis of non-model plants: a challenging but powerful approach.
abstract: Biological research has focused in the past on model organisms and most of the functional genomics studies in the field of plant sciences are still performed on model species or species that are characterized to a great extent. However, numerous non-model plants are essential as food, feed, or energy resource. Some features and processes are unique to these plant species or families and cannot be approached via a model plant. The power of all proteomic and transcriptomic methods, that is, high-throughput identification of candidate gene products, tends to be lost in non-model species due to the lack of genomic information or due to the sequence divergence to a related model organism. Nevertheless, a proteomics approach has a great potential to study non-model species. This work reviews non-model plants from a proteomic angle and provides an outline of the problems encountered when initiating the proteome analysis of a non-model organism. The review tackles problems associated with (i) sample preparation, (ii) the analysis and interpretation of a complex data set, (iii) the protein identification via MS, and (iv) data management and integration. We will illustrate the power of 2DE for non-model plants in combination with multivariate data analysis and MS/MS identification and will evaluate possible alternatives.
authors.affiliation: Division of Crop Biotechnics, K.U.Leuven, Leuven, Belgium. sebastien.carpentier@biw.kuleuven.be
authors.forename: Sebastien Christian
authors.initials: SC
authors.lastname: Carpentier
authors.forename: Bart
authors.initials: B
authors.lastname: Panis
authors.forename: Annelies
authors.initials: A
authors.lastname: Vertommen
authors.forename: Rony
authors.initials: R
authors.lastname: Swennen
authors.forename: Kjell
authors.initials: K
authors.lastname: Sergeant
authors.forename: Jenny
authors.initials: J
authors.lastname: Renaut
authors.forename: Kris
authors.initials: K
authors.lastname: Laukens
authors.forename: Erwin
authors.initials: E
authors.lastname: Witters
authors.forename: Bart
authors.initials: B
authors.lastname: Samyn
authors.forename: Bart
authors.initials: B
authors.lastname: Devreese
mesh_terms: D018506:Gene Expression Regulation, Plant; D010449:Peptide Mapping; D014674:Plant Proteins, Dietary / Q000032:analysis* / Q000737:chemistry; D010944:Plants / Q000235:genetics* / Q000378:metabolism*; D040901:Proteomics; D013048:Specimen Handling / Q000379:methods; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D014674:Plant Proteins, Dietary