Project PXD014519

Summary

Title

Metaproteomic data of maize rhizosphere

Description

We present metaproteome data from maize rhizosphere from sodic soil. Isolation of proteome from maize rhizosphere collected from Experimental Farm, ICAR-IISS, Mau, India was done with the standardized protocol at our laboratory and metaproteome analysis was done with the standardized pipepline. In total 696 proteins with different functions representing 245 genus and 395 species were identified. The proteome data provides direct evidence on the biological processes in soil ecosystem and is the first reported reference data from maize rhizosphere.

Sample Processing Protocol

Isolation of metaproteome from pooled maize rhizospheric soil samples from ICAR-IISS, Mau experimental Farm , India with the standardized protocol at our laboratory. The protein after 1D-SDS-PAGE evaluation was quantified, trypsinized and analyzed with LC/MS MS. The mass spectra were searched against the NCBInr and analysis was done with the standardized pipepline.

Data Processing Protocol

Chromatograms of the MS/MS spectra were analyzed. The raw data was processed by MassLynx 4.1 WATER software. Mascot Generic File (MGF) was generated against individual spectra. MGF file was used to search in database for protein identification on MASCOT server. Search parameters were as follows: taxonomy, all entries; fixed modification, cysteine carbamidomethylation; variable modifications, methionine oxidation; enzyme, trypsin; maximum number of missed cleavages, 1; peptide tolerance, 50 ppm; and MS/MS tolerance, 100 ppm.

Contact

Renu S, ICAR-NBAIM
Dr Renu, ICAR- National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, Mau, Uttar Pradesh, INDIA ( lab head )

Submission Date

08/07/2019

Publication Date

08/10/2019

Tissue

Not available

Instrument

Synapt MS

Software

Not available

Experiment Type

Shotgun proteomics

Publication

Publication pending