Proteomic Analysis 

NIAID Systems Virology Center (systemsvirology.org)
We welcome collaborations. When possible please notify us when our data is utilized in publications (honey@uw.edu).
Please acknowledge the Systems Virology Center, NIAID Contract No. HHSN272200800060C when using these data.

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Attached is a Word document IM001_StatisticsReport_Portal.docx outlining our method for proteomic data processing.

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Attached is an Excel spreadsheet IM001_Peptide data.xls with the normalized intensity values for all peptides that passed the filtering criteria.  Data are log base 10 intensity values, averages of technical replicates, and provided as biological replicates.  Missing values are indicated as NaN, meaning that no data were present for either technical replicate.

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Attached is an Excel spreadsheet IM001_Protein data.xls with protein values rolled up from peptide values that contained sufficient information for roll-up.  Data are log base 10 intensity values, and provided as biological replicates.  Missing values are blank cells, meaning that no data were present for any peptide for that protein for that sample.  One column indicates the number of peptides used for the protein value.

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´╗┐´╗┐Attached is an Excel spreadsheet IM001_Sig Protein list.xls, which contains all pvalues for quantitative (Dunnett's test) and qualitative (G-test) assessment of significance.  There are two worksheets: one for significant at any dose or time point and a second for those proteins that were not significant at any comparison.  The p-values are listed as: 0 (nonsignificant), 1 (significant-up regulation) and -1 (significant-down regulation).  Log base 10 ratios of each dose/time point to its time-matched mock are also included and colored for red=up and green=down by > 2fold change (log 10=0.3)

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  Attached Files  
   
 IM001_StatisticsReport_Portal.docx
 IM001_Peptide data.xls
 IM001_Protein data.xls
 IM001_Sig Protein list_Portal.xls