Computational protocol: Staphylococcus aureus Membrane-Derived Vesicles Promote Bacterial Virulence and Confer Protective Immunity in Murine Infection Models

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Protocol publication

[…] Raw data from the MS analysis was searched against NCBI S. aureus MSSA476 using the Sequest algorithm in Proteome Discoverer version 2.1 (). Data were filtered to a 1% peptide and protein level false positive rate using a reverse database approach (). The area under the curve (AUC)-based label free quantitation of detected proteins was determined through the Proteome Discoverer workflow. Proteins commonly found in the two groups (LB and BHI) and unique to each group were classified according to biological processes, molecular functions, and cellular components using DAVID (), respectively. Benjamini–Hochberg corrected p-value < 0.05 and an FDR < 5% were accepted for gene ontology (GO) terms. The computational prediction of the subcellular localization of MV proteins was performed by PSORTb (). For the appropriate input, GI numbers were converted to the UniProt ID. In total, 373 out of 639 MVs proteins were mapped into UniProtKB ID. The breakdown by localization is graphed as a pie chart. The UniProt ID was utilized to extract the protein sequence. The lipoprotein, and secretory signal peptides were predicted using PRED-LIPO (). […]

Pipeline specifications

Software tools Comet, Proteome Discoverer, DAVID, PSORTb, PRED-LIPO
Databases UniProtKB
Applications MS-based untargeted proteomics, Protein sequence analysis
Organisms Staphylococcus aureus, Bacteria, Mus musculus, Homo sapiens
Diseases Infection, Drug-Related Side Effects and Adverse Reactions