The Sample Abundances chart displays as a box-and-whisker plot the abundance of the peak intensity values for all items currently displayed on the Proteins page or the Peptide Groups page.

By default, the Sample Abundances chart displays the data for all the samples and duplicates the grouping on the Grouping & Quantification page of the analysis. Each group appears in a different color. The legend shows the colors of the sample groups.

Procedure

  1. Open the result file of interest.
  2. Select the Proteins or Peptide Groups tab.
  3. Choose View > Distribution Charts to open the Report Item Distribution chart.
  4. Select the Sample Abundances tab.
  5. (Optional) In the Color By area at the far left, select one or more of the following checkboxes to create sample groups according to the study factors for quantification:
  6. Study_factors: Lists each study factor that you defined in the study.
  7. Sample: Selects the sample mixture of all samples. The Sample checkbox is based on the Sample Type default study variable on the Grouping & Quantification page. It appears whether or not you select Sample Type on the Grouping & Quantification page.
  8. (Optional) In the Filter By area at the far left, set one or more of the following variables to filter the data:
  9. Set the Study_factor filter to On.
  10. Set the Sample filter to On.
  11. Select the arrow to the left of the On/Off filter box for Study_factor or Sample.
  12. Select the appropriate checkboxes beneath Study_factor, Sample, or both.
  13. From the Data Source list, select the result category to plot the data from, either Proteins, Peptide Groups, and the Abundance source.
  14. (Optional) To display the data in linear scale, clear the Log-Transform Data checkbox.
  15. If you do not select this checkbox, the application displays the data in linear scale.

Example Sample Abundances chart that shows the abundance of the peptides within the proteins in the samples.

Sample Abundances page of the Report Item Distribution chart.

Task

Procedure

Display the legend

Right-click the plot and choose Show Legend.

Display tooltips

Right-click the view and choose Show Position Tooltips.

The tooltips display the information in.

Zoom in

Drag your cursor to the right and select the area to enlarge in size.

Zoom out

  • Drag your cursor to the left and select the area to reduce in size.

–or–

  • Right-click the view and choose Zoom Out from the shortcut menu.

Return to the default view

Right-click the chart and choose Undo All Zoom/Pan.

Copy or save the data as an image

  • Right-click the plot and choose Copy > Image to copy an image to the Clipboard.

–or–

  • Right-click the plot and choose Export > Data As to save the data to an image file.

Copy or save the data as editable text

  • Right-click the plot and choose Copy > Data to copy the text to the Clipboard.

You can paste this text to Notepad, an Excel spreadsheet, and so on. The data appears in columnar format.

–or–

  • Right-click the plot and choose Export > Date As to save the data to a tab-delimited CSV file.

The data appears as a single column. After you transform the tab-delimited text to columns in a spreadsheet application, the spreadsheet contains two sets of columns. The first set consists of these columns from left to right: Groups, Name, Minimum Value, Maximum Value, Std. Deviation, Mean, Median, Q1 Value, Q2 Value, and Q3 Value. The second set lists the outlier data points and consists of these columns from left to right: Groups, Name, and Outlier.

View the table row for an outlier data point

In the plot, double-click the data point.

Select the checkbox for an outlier data point

In the plot, right-click the data point and choose Check Point.

In the result table, the checkbox is selected for the corresponding compound or expected compound.

Clear the checkbox for an outlier data point

Right-click the data point in the volcano plot, and choose Uncheck Point.

Select the checkboxes for all of the visible data points

Right-click the plot and choose Check All Visible Points.

Clear all visible data points

Right-click the plot and choose Uncheck All Visible Points.