This section shows how to access and filter the results of the analysis.

NOTE

Periodically, the FASTA files provided by the Annotation Server or UniProt are updated. The minor changes in an updated file cause minor changes in the results. The changes are not important in this context. Your results will be nearly identical.

Procedure

  1. Access the results by using one of the following methods.
  2. Select the Analysis Results tab in the study, and do one of the following:
    - Double-click the row for the result ID 1.
    - Highlight the row, and select Open Result to open the result file in a separate tab.
  4. Open the job queue by choosing Administration > Show Job Queue, and do one of the following:
    - Double-click the row in the Job Queue for the Consensus workflow that just finished.
    - Select the row, and select Open Results to open the results in a separate tab.
  6. In Windows Explorer, find the study folder, and double-click the result file.
  7. View the volcano plot.
  8. Select Report Item Distribution View.
  9. Select the Volcano Plots tab.
  10. Ensure that the Data Source shows Peptide Groups and the Comparison shows IGF-1 vs. Contro.
  11. Double-click the identified point in the volcano plot.
  12. The peptide group associated with that point is highlighted.
  14. At the bottom of the Peptide Groups pane, select Show Associated Tables, and ensure that the Proteins table is selected.
  16. The highlighted peptide is for a phosphorylation site on the insulin growth receptor factor 1 receptor, which is the cell surface protein that is targeted by IGF-1.
  18. Close the Report Item Distribution chart.
  19. Select Hide Associated Tables between the Peptide Groups table and the associated Proteins table.
  20. To get a list of differentially expressed post-translational modifications identified in the run:
  21. In the main result table, select the Peptide Groups tab.
  22. Select Filter .
  23. In the Display Filter pane, select Add Property, and select the Abundance Ratio Adj. p-value filter.
  25. In the Add property dropdown menus, select Abundance Ratio Adj. P-Value > is less than > 0.01 > in ratio > IGF-1/Control.
  26. Select Apply.
  28. Select Filter to close the Display Filters pane.
  29. Right-click the Peptide Groups table, and select Check All > In This and All Associated Tables.
  31. Go to the Modification Sites Table.
  32. Sort the table by selecting the Checked column header.
  33. The phosphorylation sites for peptides that are significantly differentially expressed are shown in the table.
  34. To view enriched pathways and gene ontology terms associated with the proteins checked in the previous step:
  35. Select Enrichment .
  36. For Background, select All Identifiable Proteins from All Identified Proteins.
  37. For Annotation, select Reactome Pathways from Gene Ontology - All Terms.
  38. The list of terms automatically updates after changing the data source.