MassIVE MSV000089984

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Top-down proteomics and intact protein imaging of soybean root nodules infected with Bradyrhizobium japonicum

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Description

Global top-down proteomics LCMS analysis of proteins purified from soybean root nodules infected with either WT or nifH- mutant Bradyrhizobium japonicum. Raw LCMS data were processed with TopPIC; combined proteoform-spectral-matches, and label free quantitation results are included as separate csv files ("*_all_PrSMs.csv", "*_LFQ_Table.csv"). Also includes MALDI-Orbitrap data of intact proteins. The MALDI raw files and xml files can be loaded into imaging software for viewing ion images. Representative summed spectra are included separately in two "IMAGE-avg11567_from100to200min.raw" files. More detailed analysis and representative proteoform ion images are discussed in the associated manuscript. For sample processing, frozen tissue were homogenized for LCMS and proteins were extracted with the MPlex protocol. For MALDI, frozen tissues were sliced and embedded on ITO slides and sprayed with DHA matrix. LCMS data were processed with TopPIC and TopPICR. Imaging data were collected with Spectroglyph software. [doi:10.25345/C5HM52P7F] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: plant ; top-down proteomics ; soybean root nodule ; proteoform ; symbiosis

Contact

Principal Investigators:
(in alphabetical order) 		Mowei Zhou, Pacific Northwest National Laboratory, United States
Submitting User: alchemistmatt

Publications

Mowei Zhou, James M. Fulcher, Kevin J. Zemaitis, David J. Degnan, Yen-Chen Liao, Marija Velickovic, Dusan Velickovic, Lisa M. Bramer, William R Kew, Gary Stacey, Ljiljana Pasa-Tolic.
Discovery top-down proteomics in symbiotic soybean root nodules.
Front. Anal. Sci., 30 September 2022. doi: 10.3389/frans.2022.1012707.

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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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