title: The role of proteomics in progressing insights into plant secondary metabolism.
abstract: The development of omics has enabled the genome-wide exploration of all kinds of biological processes at the molecular level. Almost every field of plant biology has been analyzed at the genomic, transcriptomic and proteomic level. Here we focus on the particular contribution that proteomic technologies have made in progressing knowledge and characterising plant secondary metabolism (SM) pathways since early expectations were created 15 years ago. We analyzed how three major issues in the proteomic analysis of plant SM have been implemented in various research studies. These issues are: (i) the selection of a suitable plant material rich in secondary metabolites of interest, such as specialized tissues and organs, and in vitro cell cultures; (ii) the proteomic strategy to access target proteins, either a comprehensive or a differential analysis; (iii) the proteomic approach, represented by the hypothesis-free discovery proteomics and the hypothesis-driven targeted proteomics. We also examine to what extent the most-advanced technologies have been incorporated into proteomic research in plant SM and highlight some cutting edge techniques that would strongly benefit the progress made in this field.
authors.affiliation: Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies "Ramon Margalef", University of Alicante , Alicante, Spain.
authors.forename: María J
authors.initials: MJ
authors.lastname: Martínez-Esteso
authors.affiliation: Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies "Ramon Margalef", University of Alicante , Alicante, Spain.
authors.forename: Ascensión
authors.initials: A
authors.lastname: Martínez-Márquez
authors.affiliation: Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies "Ramon Margalef", University of Alicante , Alicante, Spain ; Biotechnology and Molecular Biology Group, Quevedo State Technical University , Quevedo, Ecuador.
authors.forename: Susana
authors.initials: S
authors.lastname: Sellés-Marchart
authors.affiliation: Proteomics and Genomics Division, Research Technical Facility, University of Alicante , Alicante, Spain.
authors.forename: Jaime A
authors.initials: JA
authors.lastname: Morante-Carriel
authors.affiliation: Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies "Ramon Margalef", University of Alicante , Alicante, Spain.
authors.forename: Roque
authors.initials: R
authors.lastname: Bru-Martínez
keywords: DIGE; MRM; alkaloids; cell cultures; polyphenols; secondary metabolism; shotgun proteomics; terpenoids