PXD026369 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Optimization of protein extraction methods for root-associated microbes in maize |
Description | The goal of this study was to optimize protein extraction methods to study root-associated bacteria in maize. For this we inoculated sterile maize plants with a synthetic community composed of seven different bacteria (Ben Niu et al. PNAS 2017, vol 114, n 12). Then, we extracted proteins from maize roots using eight different protein extraction methods 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 vortexing maize roots with glass beads in PBS yielded the highest numbers of microbial protein identification. |
HostingRepository | PRIDE |
AnnounceDate | 2022-09-08 |
AnnouncementXML | Submission_2022-09-08_11:52:24.073.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Fernanda Salvato |
SpeciesList | scientific name: Chryseobacterium indologenes; NCBI TaxID: 253; scientific name: Enterobacter ludwigii; NCBI TaxID: 299767; scientific name: Ochrobactrum pituitosum; NCBI TaxID: 571256; scientific name: Pseudomonas putida; NCBI TaxID: 303; scientific name: Herbaspirillum robiniae; NCBI TaxID: 2014887; scientific name: Zea mays (Maize); NCBI TaxID: 4577; scientific name: Curtobacterium pusillum; NCBI TaxID: 69373; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-05-31 06:56:06 | ID requested | |
⏵ 1 | 2022-09-08 11:52:24 | 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: Maize, corn, 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
- PXD026369
- Label: PRIDE project
- Name: Optimization of protein extraction methods for root-associated microbes in maize