title: Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves.
abstract: Protein phosphorylation is one of the most common post-translational modifications (PTMs), which can regulate protein activity and localization as well as protein-protein interactions in numerous cellular processes. Phosphopeptide enrichment techniques enable plant researchers to acquire insight into phosphorylation-controlled signaling networks in various plant species. Most phosphoproteome analyses of plant samples still involve stable isotope labeling, peptide fractionation, and demand a lot of mass spectrometry (MS) time. Here, we present a simple workflow to probe, map, and catalogue plant phosphoproteomes, requiring relatively low amounts of starting material, no labeling, no fractionation, and no excessive analysis time. Following optimization of the different experimental steps on Arabidopsis thaliana samples, we transferred our workflow to maize, a major monocot crop, to study signaling upon drought stress. In addition, we included normalization to protein abundance to identify true phosphorylation changes. Overall, we identified a set of new phosphosites in both Arabidopsis thaliana and maize, some of which are differentially phosphorylated upon drought. All data are available via ProteomeXchange with identifier PXD003634, but to provide easy access to our model plant and crop data sets, we created an online database, Plant PTM Viewer ( bioinformatics.psb.ugent.be/webtools/ptm_viewer/ ), where all phosphosites identified in our study can be consulted.
authors.affiliation: Department of Plant Systems Biology, VIB , 9052 Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium.|Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.|Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.
authors.forename: Lam Dai
authors.initials: LD
authors.lastname: Vu
authors.affiliation: Department of Plant Systems Biology, VIB , 9052 Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium.|Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.|Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Stes
authors.affiliation: Department of Plant Systems Biology, VIB , 9052 Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium.
authors.forename: Michiel
authors.initials: M
authors.lastname: Van Bel
authors.affiliation: Department of Plant Systems Biology, VIB , 9052 Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium.
authors.forename: Hilde
authors.initials: H
authors.lastname: Nelissen
authors.affiliation: Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.|Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.
authors.forename: Davy
authors.initials: D
authors.lastname: Maddelein
authors.affiliation: Department of Plant Systems Biology, VIB , 9052 Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Inzé
authors.affiliation: Department of Plant Systems Biology, VIB , 9052 Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium.
authors.forename: Frederik
authors.initials: F
authors.lastname: Coppens
authors.affiliation: Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.|Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.affiliation: Medical Biotechnology Center, VIB , 9000 Ghent, Belgium.|Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.
authors.forename: Kris
authors.initials: K
authors.lastname: Gevaert
authors.affiliation: Department of Plant Systems Biology, VIB , 9052 Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium.
authors.forename: Ive
authors.initials: I
authors.lastname: De Smet
mesh_terms: D017360:Arabidopsis / Q000378:metabolism; D001665:Binding Sites; D055864:Droughts; D010750:Phosphoproteins / Q000032:analysis*; D010766:Phosphorylation; D018515:Plant Leaves / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D015398:Signal Transduction; D057188:Workflow; D003313:Zea mays / Q000737:chemistry / Q000378:metabolism*
chemical_list: D010750:Phosphoproteins
keywords: Arabidopsis; database; drought stress; maize; phosphoproteomics