title: In-depth characterization of the tomato fruit pericarp proteome.
abstract: Since the genome of Solanum lycopersicum L. was published in 2012, some studies have explored its proteome although with a limited depth. In this work, we present an extended characterization of the proteome of the tomato pericarp at its ripe red stage. Fractionation of tryptic peptides generated from pericarp proteins by off-line high-pH reverse-phase phase chromatography in combination with LC-MS/MS analysis on a Fisher Scientific Q Exactive and a Sciex Triple-TOF 6600 resulted in the identification of 8588 proteins with a 1% FDR both at the peptide and protein levels. Proteins were mapped through GO and KEGG databases and a large number of the identified proteins were associated with cytoplasmic organelles and metabolic pathways categories. These results constitute one of the most extensive proteome datasets of tomato so far and provide an experimental confirmation of the existence of a high number of theoretically predicted proteins. All MS data are available in the ProteomeXchange repository with the dataset identifiers PXD004947 and PXD004932.
authors.affiliation: BIOSYST-MeBioS, KU Leuven, Leuven, Belgium.
authors.forename: Clara I
authors.initials: CI
authors.lastname: Mata
authors.affiliation: Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Fabre
authors.affiliation: BIOSYST-MeBioS, KU Leuven, Leuven, Belgium.
authors.forename: Maarten L A T M
authors.initials: ML
authors.lastname: Hertog
authors.affiliation: Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Harriet T
authors.initials: HT
authors.lastname: Parsons
authors.affiliation: Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Deery
authors.affiliation: Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Kathryn S
authors.initials: KS
authors.lastname: Lilley
authors.affiliation: BIOSYST-MeBioS, KU Leuven, Leuven, Belgium.
authors.forename: Bart M
authors.initials: BM
authors.lastname: Nicolaï
mesh_terms: D002853:Chromatography, Liquid; D005638:Fruit / Q000378:metabolism*; D018551:Solanum lycopersicum / Q000378:metabolism*; D010940:Plant Proteins / Q000378:metabolism; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics; D053719:Tandem Mass Spectrometry
chemical_list: D010940:Plant Proteins; D020543:Proteome
keywords: MS; Plant proteomics; Solanum lycopersicum L; Tomato