MassIVE MSV000088754

Partial Public

Shotgun proteomics of soybean root nodules infected by Bradyrhizobium japonicum

Description

Global bottom-up proteomics analysis of proteins purified from soybean root nodules infected with either WT or nifH- mutant Bradyrhizobium japonicum. Nine glycoproteins containing Lewis-a N-glycans, with 3 distinct Lewis-a epitopes (Hex:5 HexNAc:4 dHex:3 Pent:1, Hex:4 HexNAc:4 dHex:2 Pent:1, and Hex:4 HexNAc:3 dHex:2 Pent:1) were observed. Proteins purified from WT and nifH- infected soybean root nodules (five biological replicates each) were reduced using dithiothreitol, alkylated with iodoacetamide and trypsin digested followed by C18 SPE clean-up and LC-MS/MS analysis. Raw data files were processed using FragPipe v17.1, then output files 'combined_modified_peptide.tsv' and 'combined_protein.tsv' were used to identify glycopeptides and for global protein quantitation. These files, along with Excel files containing global quantitation analysis files for soybean nodule (Glycine max) and bacterial (Bradyrhizobium), are available in directory 'Quantification/MSFragger_results'. Glycopeptide data were also processed with PMI Byonic, and Excel file results are available in directory 'Quantification/PMI_Byonic_results'. [doi:10.25345/C5NG4R] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: plant ; N-glycans ; glycoprotein ; soybean root nodule

Contact

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

Publications

Veli?kovi? D, Liao YC, Thibert S, Veli?kovi? M, Anderton C, Voglmeir J, Stacey G, Zhou M.
Spatial Mapping of Plant N-Glycosylation Cellular Heterogeneity Inside Soybean Root Nodules Provided Insights Into Legume-Rhizobia Symbiosis.
Front Plant Sci. Epub 2022 May 16.

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