Shotgun proteomics of soybean root nodules infected by Bradyrhizobium japonicum

ABSTRACT: 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'.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Glycine Max (ncbitaxon:3847)

SUBMITTER: Mowei Zhou  

PROVIDER: MSV000088754 | MassIVE | Mon Jan 31 13:54:00 GMT 2022

REPOSITORIES: MassIVE