title: From Phosphoproteome to Modeling of Plant Signaling Pathways.
abstract: Quantitative proteomic experiments in recent years became almost routine in many aspects of biology. Particularly the quantification of peptides and corresponding phosphorylated counterparts from a single experiment is highly important for understanding of dynamics of signaling pathways. We developed an analytical method to quantify phosphopeptides (pP) in relation to the quantity of the corresponding non-phosphorylated parent peptides (P). We used mixed-mode solid-phase extraction to purify total peptides from tryptic digest and separated them from most of the phosphorous-containing compounds (e.g., phospholipids, nucleotides) which enhances pP enrichment on TiO2 beads. Phosphoproteomic data derived with this designed method allows quantifying pP/P stoichiometry, and qualifying experimental data for mathematical modeling.
authors.affiliation: Plant Systems Biology, Plant Physiology, University of Hohenheim, Fruwirthstrasse 12, 70599, Stuttgart, Germany. maksim.zakhartsev@uni-hohenheim.de.
authors.forename: Maksim
authors.initials: M
authors.lastname: Zakhartsev
authors.affiliation: Plant Systems Biology, Plant Physiology, University of Hohenheim, Fruwirthstrasse 12, 70599, Stuttgart, Germany.
authors.forename: Heidi
authors.initials: H
authors.lastname: Pertl-Obermeyer
authors.affiliation: Plant Systems Biology, Plant Physiology, University of Hohenheim, Fruwirthstrasse 12, 70599, Stuttgart, Germany.
authors.forename: Waltraud X
authors.initials: WX
authors.lastname: Schulze
mesh_terms: D002853:Chromatography, Liquid; D008954:Models, Biological; D010748:Phosphopeptides / Q000737:chemistry / Q000378:metabolism; D010750:Phosphoproteins / Q000737:chemistry / Q000378:metabolism*; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism*; D010944:Plants / Q000378:metabolism*; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D015398:Signal Transduction; D052616:Solid Phase Extraction; D053719:Tandem Mass Spectrometry
chemical_list: D010748:Phosphopeptides; D010750:Phosphoproteins; D010940:Plant Proteins; D020543:Proteome
keywords: Mathematical modeling; Metal oxide affinity chromatography; Mixed-mode solid-phase extraction; Phosphopeptide enrichment