Project ID: IPD9282

Project Title: Proteins from Outer Membrane Vesicules of Pseudomonas syringae Lz4W

Principal Investigator: Dr. Medicharla Venkata Jagannadham

PI Affiliation: Chief Scientist, CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India

Description: The proteins from Outer Membrane Vesicles (OMVs) were extracted by chilled acetone method. The proteins were separated on 1D SDS-PAGE (12%). From the gel, total 10 fractions were made and all of them were subjected to in gel digestion using trypsin. The MS/MS spectra of the resulting tryptic peptides were recordedby using LC coupled ESI-MS/MS (Thermo Orbitrap Velos). The mass spectral data thus obtained was analysed by using Proteome Discoverer 1.3. Since the genome sequence of P. syringae Lz4W is not available, the data was searched against a database prepared from 20 related Pseudomonas species whose genome sequence is available on Uniprot (Updated upto Jan 2013). The search was observed by using nodes Sequest and Mascot both, the enzyme selected was trypsin with maximum 2 missed cleavages, the precursor tolerance set at 10 ppm, fragment tolerance at 0.8 Da, carbamidomethylated cystein (57.02 Da) as fixed modification, oxidised methionine (15.99 Da) as variable modification. After the search is over, the results were refined applying result filters as Peptide confidence (High) and Differentiable Proteins (including distinct proteins), which makes sure that each protein entry in the list is identified with at least one unique peptide.

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Meta Data

Sample Preparation: A cell lysate (CL) of P. syringae Lz4W was prepared as described earlier. See details in reference(s):

Peptide Separation: The proteins from OMV of P. syringae Lz4W were separated on a one-dimensional (1D) gel, excised into 8–10 pieces, and digested with trypsin using standard protocols.See details in reference(s):

Protein Characterization: A cell lysate (CL) of P. syringae Lz4W was prepared as described earlier. See details in reference(s):

Experiment Type: Bottom-up

PubMed-ID: 24437924

Species: Pseudomonas sp.-306

Tissue: Unknown

Cell Type: Unknown

Disease: Unknown

Instrument Details: LTQ Orbitrap Velos (MS:1001742)

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