PXD039004

PXD039004 is an original dataset announced via ProteomeXchange.

Title	Short Gradient Multi-CV FAIMSpro BoxCar DIA Facilitates Quantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana - Abiotic Stress Dataset
Description	A major limitation in quantitative time-course proteomics is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity, high dynamic samples such as plant extracts, this is tradeoff is especially apparent. To address this, we evaluate multiple composition voltage (CV) High Field Asymetric Waveform Ion Mobility Spectrometry (FAIMSpro) settings using the latest label-free, single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply-quantify the Arabidopsis thaliana seedling proteome at microliter per minute flow rates. Using a micro-flow BoxCar DIA acquisition workflow with -30, -50, -70 CV FAIMSpro settings we are able to consistently quantify >5000 Arabidopsis seedling proteins over a 21-minute gradient, facilitating the analysis of ~48 samples per day. Utilizing this acquisition approach, we next performed an abiotic stress time-course experiment, whereby we quantified proteome-level changes occurring in Arabidopsis seedling shoots and roots over 24 h of salt and osmotic stress. Here, we successfully quantify over >6400 shoot and >8500 root protein groups, respectively, quantifying nearly 9700 unique protein groups total across the study. Collectively, we pioneer a fast-flow, multi-CV FAIMSpro BoxCar DIA acquisition workflow that represents an exciting new analysis approach for quantitative time-course proteomics experimentation in plants.
HostingRepository	PRIDE
AnnounceDate	2024-01-26
AnnouncementXML	Submission_2024-01-26_09:56:52.791.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Richard Uhrig
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-20 20:34:05	ID requested
⏵ 1	2024-01-26 09:56:54	announced

10.1016/j.mcpro.2023.100638;

Rodriguez Gallo MC, Li Q, Talasila M, Uhrig RG, Quantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana Using Short Gradient Multi-CV FAIMSpro BoxCar DIA. Mol Cell Proteomics, 22(11):100638(2023) [pubmed]

submitter keyword: BoxCarDIA, FAIMSpro, Arabidopsis thaliana, DirectDIA

Richard Glen Uhrig
contact affiliation	Depamrtment of Biological Sciences - University of Alberta
contact email	ruhrig@ualberta.ca
lab head
Richard Uhrig
contact affiliation	University of Alberta
contact email	ruhrig@ualberta.ca
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/2024/01/PXD039004

PRIDE project URI

• PRIDE
  1. PXD039004
     1. Label: PRIDE project
     2. Name: Short Gradient Multi-CV FAIMSpro BoxCar DIA Facilitates Quantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana - Abiotic Stress Dataset