The Trend chart shows the abundance of proteins or peptide groups across all sample groups. It displays the data as a trend line for each protein or peptide group. You define the sample groups by selecting one or more checkboxes under Group By in the collapsible pane to the left of the chart.

The result file must contain multiple quantification values if you want to display a trend chart.

Procedure

  1. Open the result file of interest.
  2. Select the Proteins or Peptide Groups tab.
  3. Select the protein or peptide group of interest.
  4. Select View > Trend Chart, or select Trend Chart View .
  5. The Trend Chart opens as a docked window at the bottom of the result pages. This example shows five groups of mitochondrial proteins increasing in relative abundance over time.
  6. Trend chart
  7. If the active result table does not contain a quantification results, the following text appears in the graph area:
  8. - No Results Available to Plot.
  9. To plot the peak areas for more proteins or peptide groups, press the CTRL key and select one or more rows in the results table, taking care to avoid selecting an editable table cell.
  10. (Optional) In the Group By area at the far left, select the appropriate checkboxes to specify how to create sample groups from the data:
  11. Study_factors: Creates sample groups according to the study factors that you defined in the study.
  12. File: Creates sample groups according to file.
  13. Quan Channel: Creates sample groups according to quantification channel.
  14. Sample: Creates sample groups according to the sample type study variable.
  15. (Optional) In the Filter By area at the far left, specify how to filter the data. Set the type of filter to On, select the arrow to the left of the On/Off filter box, and select the appropriate study factors, input files, quantification channels, or samples.
  16. Study_factor: Filters by study factor, for example, Time (days).
  17. File: Filters by input file.
  18. Quan Channel: Filters by quantification channel.
  19. Sample filter: Filters by sample.
  20. (Optional) Select the Use Normalized Abundances checkbox to display the normalized abundances.
  21. The checkbox is available if the Reporter Ions Quantifier node or the Precursor Ions Quantifier node normalized the quantification data because you set the Normalization Mode parameter to Total Peptide Amount or Specific Protein Amount.
  22. If you do not select the Use Normalized Abundances checkbox, the application displays the absolute abundance values at each study factor point.
  23. (Optional) From the Scaling menu, choose a value by which to scale the abundance values represented by the trend line.
  24. This value resets the height of the trend line and changes the y axis. Especially when you select a number of proteins to view in the Trend chart, rescaling makes it easier to compare the trend lines and interpret the results.
  25. Unscaled: Uses absolute abundance values and displays the raw abundance values at each study factor point.
  26. Scaled: Displays scaled abundance values.
  27. Scaled to x: Scales the points in the trend line to a selected study factor.
  28. If you selected Show Legend from the shortcut menu (right-click the Trend chart), the legend displays the name and color of each selected protein or peptide group.