title: Label-free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development.
abstract: Current innovations in mass-spectrometry-based technologies allow deep coverage of protein expression. Despite its immense value and in contrast to transcriptomics, only a handful of studies in crop plants engaged with global proteome assays. Here, we present large-scale shotgun proteomics profiling of tomato fruit across two key tissues and five developmental stages. A total of 7738 individual protein groups were identified and reliably measured at least in one of the analyzed tissues or stages. The depth of our assay enabled identification of 61 differentially expressed transcription factors, including renowned ripening-related regulators and elements of ethylene signaling. Significantly, we measured proteins involved in 83% of all predicted enzymatic reactions in the tomato metabolic network. Hence, proteins representing almost the complete set of reactions in major metabolic pathways were identified, including the cytosolic and plastidic isoprenoid and the phenylpropanoid pathways. Furthermore, the data allowed us to discern between protein isoforms according to expression patterns, which is most significant in light of the weak transcript-protein expression correspondence. Finally, visualization of changes in protein abundance associated with a particular process provided us with a unique view of skin and flesh tissues in developing fruit. This study adds a new dimension to the existing genomic, transcriptomic and metabolomic resources. It is therefore likely to promote translational and post-translational research in tomato and additional species, which is presently focused on transcription.
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.|Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel.
authors.forename: Jedrzej
authors.identifier: http://orcid.org/0000-0003-1086-0920
authors.initials: J
authors.lastname: Szymanski
authors.affiliation: The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel.
authors.forename: Yishai
authors.initials: Y
authors.lastname: Levin
authors.affiliation: The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel.
authors.forename: Alon
authors.initials: A
authors.lastname: Savidor
authors.affiliation: Metabolic Biology Department, John Innes Centre, Norwich, NR4 7UH, UK.
authors.forename: Dario
authors.initials: D
authors.lastname: Breitel
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
authors.forename: Louise
authors.initials: L
authors.lastname: Chappell-Maor
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
authors.forename: Uwe
authors.initials: U
authors.lastname: Heinig
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
authors.forename: Nadine
authors.initials: N
authors.lastname: Töpfer
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
authors.forename: Asaph
authors.initials: A
authors.lastname: Aharoni
mesh_terms: D005638:Fruit / Q000235:genetics / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D018551:Solanum lycopersicum / Q000235:genetics / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods*
chemical_list: D010940:Plant Proteins; D020543:Proteome
keywords: 
  Solanum lycopersicum
  ; fruit development; fruit ripening; proteomics; secondary metabolism