The following table describes the parameters on the Trend chart.

Trend Chart parameters

Parameter

Description

Group By

Creates sample groups according to the following variables:

  • Study_factor: Creates sample groups according to the study factors that you defined in the study.
  • File: Creates sample groups according to file.
  • Quan Channel: Creates sample groups according to quantification channel.
  • Sample: Creates sample groups according to the sample type study variable.

Filter By

Filters the data according to the following filter types:

  • Study_factor: Filters by study factor, for example, Time (days).
  • File: Filters by input file.
  • Quan Channel: Filters by quantification channel.
  • Sample filter: Filters by sample.

Scaling

Determines whether and how the application scales the abundance values in the trend line.

  • Unscaled: Uses absolute abundance values and displays the raw abundance values at each study factor point.
  • Scaled: Displays scaled abundance values.
  • Scaled to x: Scales the points in the trend line to a selected study factor.

Use Normalized Abundances

Determines whether the chart displays normalized abundances.

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.

  • Selected: Displays normalized abundances.
  • Clear: Displays the absolute abundance values at each study factor point.

Groups (x-axis)

Displays the groups selected in the study—that is, the available study factors when the run starts.

Abundances (y-axis)

Displays the abundance of proteins or peptide groups.