Computational protocol: Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences

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Protocol publication

[…] Proteins were identified and analyzed as previously described []. All searches were done using TurboSEQUEST™ (Bioworks Browser 3.2; ThermoElectron) []. Mass spectra and tandem mass spectra were searched against an in silico trypsin-digested non-redundant protein database of Bos taurus downloaded from National Center for Biotechnology Institute (NCBI). Cysteine carboxyamidomethylation and methionine single and double oxidation were included in the search criteria. Decoy searches from a randomized version of the bovine protein database were conducted with tandem mass spectra as described above. The probability for peptide identification was estimated using a method described for Sequest data analysis and was set at p < 0.05 []. Probabilities of protein identifications being incorrect were calculated using published methods [,]. Differential protein expression analysis based on ΣXcorr was carried out as described in ProtQuant []. To correct for multiple testing, we determined the false discovery rate (FDR) for p value using published methods []. [...] Gene ontology (GO) analysis was carried using AgBase tools [] to identify the molecular functions, biological processes and cellular component represented in our protein datasets. GORetriver tool was used to obtain all pre-existing GO annotations available for known proteins in our datasets. In addition, we used GOanna to provide additional GO annotation (i.e. predicted based on sequence orthologes and analysis of functional domains) for bovine proteins without existing annotation. All GO annotations for our datasets were grouped into more generalized categories using GOSlimViewer and summarized using the GOA and Whole Proteome GOSlim set. Subcategories in each of the three GOSlim functional categories are shown as a fold change between the percentages of GO terms identified in cp to those of ncp BVDV-infected monocytes in Figure . […]

Pipeline specifications

Software tools Comet, Goanna, GOSlimViewer
Databases AgBase
Applications MS-based untargeted proteomics, Amino acid sequence alignment
Organisms Bos taurus, Bovine viral diarrhea virus 1
Diseases Hepatitis, Viral, Human, Immunologic Deficiency Syndromes, Infection, Multiple Sclerosis, Virus Diseases, Genetic Diseases, Inborn