PXD004887

PXD004887 is an original dataset announced via ProteomeXchange.

Title	Large-scale Perspective on Protein Dynamics in Tomato Fruit Tissues Development through Label-free Deep Shotgun Proteomics
Description	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 Arabidopsis and especially other plant species engaged with global proteome assays. Here, we present large-scale protein profiling of tomato fruit across two key tissues and five developmental stages. This was accomplished by means of a shotgun proteomic assay comprising prior multi-step peptide fractionation followed by nano flow liquid chromatography coupled with high-resolution mass-spectrometry. A total of 7738 individual proteins were identified and reliably measured at least in one of the analysed tissues or stages. The detection of 115 putative transcription factors (TFs) further demonstrated the depth of our assay since a small number of TF proteins are typically detected in plant proteomics assays. Among this TFs set, 61 were differentially expressed in fruit development including renowned ripening regulators and elements of ethylene signalling. Curiously, we measured more than 80% of the predicted enzymatic reactions in the tomato metabolic network. Hence, proteins representing almost the complete set of reactions in major metabolic pathways were detected 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, protein level view of skin and flesh tissues in developing fruit. This study adds a different perspective 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.
HostingRepository	PRIDE
AnnounceDate	2017-01-30
AnnouncementXML	Submission_2017-01-30_09:49:07.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yishai Levin
SpeciesList	scientific name: Solanum lycopersicum; NCBI TaxID: 4081;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-08-23 03:16:07	ID requested
⏵ 1	2017-01-30 09:49:08	announced

Szymanski J, Levin Y, Savidor A, Breitel D, Chappell-Maor L, Heinig U, T, ö, pfer N, Aharoni A, Label-free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development. Plant J, 90(2):396-417(2017) [pubmed]

curator keyword: Biological

submitter keyword: Solanum lycopersicum, proteomics, fruit, development, ripening

Asaph Aharoni
contact affiliation	Weizmann Institute of Science
contact email	asaph.aharoni@weizmann.ac.il
lab head
Yishai Levin
contact affiliation	Weizmann Institute of Science, Israel
contact email	yishai.levin@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD004887
     1. Label: PRIDE project
     2. Name: Large-scale Perspective on Protein Dynamics in Tomato Fruit Tissues Development through Label-free Deep Shotgun Proteomics