PXD026330

PXD026330 is an original dataset announced via ProteomeXchange.

Title	Optimization of protein extraction methods for root-associated microbes in Arabidopsis
Description	The goal of this study was to optimize protein extraction methods to study root-associated bacteria in Arabidopsis. For this we inoculated Arabidopsis seedlings grown in agar plates with a synthetic community (SynSom) composed of four different strains (Variovorax paradoxus, Arthrobacter sp, Agrobacterium sp. and Pseudomonas sp.. Twelve days after inoculation we extracted proteins from the roots using six different protein extraction methods each in triplicates. These methods were a combination of different extraction buffers (SDS or Triton-based) and mechanical disruption methods (bead-beating, N2 grinding, glass homogenizer and freeze-thaw cycles) We found that bead-beating the roots with lysing matrix E in SDT lysis buffer yielded the highest numbers of microbial protein identification and enhanced the detection of proteins derived from gram positive bacteria.
HostingRepository	PRIDE
AnnounceDate	2022-09-08
AnnouncementXML	Submission_2022-09-08_11:41:24.668.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fernanda Salvato
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Arthrobacter; NCBI TaxID: 1663; scientific name: Variovorax paradoxus; NCBI TaxID: 34073; scientific name: Agrobacterium; NCBI TaxID: 357; scientific name: Pseudomonas; NCBI TaxID: 286;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-27 22:58:00	ID requested
⏵ 1	2022-09-08 11:41:25	announced

Salvato F, Vintila S, Finkel OM, Dangl JL, Kleiner M, Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes. Mol Plant Microbe Interact, 35(11):977-988(2022) [pubmed]

submitter keyword: Arabidopsis, metaproteomics, metaproteome, roots, protein extraction, plant-microbe interactions, plant microbiota, microbiome

Manuel Kleiner
contact affiliation	North Carolina State University
contact email	manuel_kleiner@ncsu.edu
lab head
Fernanda Salvato
contact affiliation	North Carolina State University
contact email	fersalvato@gmail.com
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/2022/09/PXD026330

PRIDE project URI

• PRIDE
  1. PXD026330
     1. Label: PRIDE project
     2. Name: Optimization of protein extraction methods for root-associated microbes in Arabidopsis