PXD031100

PXD031100 is an original dataset announced via ProteomeXchange.

Title	Identification of novel peptide forms associated with seasonality and water restriction imposition in Eucalyptus grandis leaf proteome
Description	Climate change is escalating the frequency and intensity of warming and drought periods around the globe, currently representing a threat to many plant species. Understanding how plants cope with all those abiotic factors are indeed crucial. Here, we investigate how Eucalyptus grandis, a plant genus with several industry applications, cope with seasonal variation and water restriction imposition at their proteomic level under field conditions. For that, we attempted to confidently identify known proteins and novel peptides associated with the effect of seasonality and water restriction impositions, as well as to provide insights into how novel peptides behave under such conditions. Leaf proteome of E. grandis plants was studied under both a conventional proteomic workflow and a dedicated proteogenomics approach. The highest proteomic variability was identified in the summer season and the most abundant known proteins associated with seasonal variation were related to the photosynthesis process. Post-translational modifications, protein turnovers, and chaperones were the main functional classifications identified among biological treatments. Furthermore, we were able to identify 144 novel peptides by both spectral correlations against modified databases (43) and by a de novo peptide sequencing approach (101) not predicted by current proteomics pipelines. We believe that most single amino acid substituted (SAS) peptides, mainly associated with the photosynthesis process, decreased the protein stability by altering the quantitative change upon ΔΔG values and non-covalent interactions. MRM validation assays were performed for selected novel peptide identifications to provide an extra level of evidence showing to be a very robust mass-spectrometry method of validation.
HostingRepository	PRIDE
AnnounceDate	2024-03-25
AnnouncementXML	Submission_2024-03-25_10:24:44.572.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gabriel Jorge
SpeciesList	scientific name: Eucalyptus grandis; NCBI TaxID: 71139;
ModificationList	No PTMs are included in the dataset
Instrument	TSQ Quantiva; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-19 09:39:44	ID requested
⏵ 1	2024-03-25 10:24:44	announced

10.1016/J.CPB.2023.100286;

submitter keyword: drought stress, MRM.,Proteomics, Proteogenomics

Tiago Santana Balbuena
contact affiliation	Sao Paulo State University, Department of Technology, Jaboticabal, Sao Paulo, Brazil
contact email	tiago.balbuena@unesp.br
lab head
Gabriel Jorge
contact affiliation	University of Missouri
contact email	gabriel.lemes@unesp.br
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/03/PXD031100

PRIDE project URI

• PRIDE
  1. PXD031100
     1. Label: PRIDE project
     2. Name: Identification of novel peptide forms associated with seasonality and water restriction imposition in Eucalyptus grandis leaf proteome