PXD026330 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-05-27 22:58:00 | ID requested | |
⏵ 1 | 2022-09-08 11:41:25 | announced | |
Publication List
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] |
Keyword List
submitter keyword: Arabidopsis, metaproteomics, metaproteome, roots, protein extraction, plant-microbe interactions, plant microbiota, microbiome |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD026330
- Label: PRIDE project
- Name: Optimization of protein extraction methods for root-associated microbes in Arabidopsis