The following table lists the parameters in the PCA Plots view of the Report Item Distribution chart.

Parameters in the PCA Plots view of the Report Item Distribution chart

Parameter

Description

Group By

Creates sample groups according to the study factors for quantification:

  • Study_factors: Lists each study factor that you defined in the study.
  • 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.

The Group By parameter only applies to the plots on the Scores Plot page.

Filter By

Filters the data according to the following variables:

  • Study_factors: Filters by the study factor that you defined in the study.
  • Sample: Filters by sample (see the description of Sample for the Group By parameter).

The Filter By parameter only applies to the plots on the Scores Plot page and the Loadings Plot page.

Data Source

Specifies the result category to plot the data from:

  • Proteins: From protein data.
  • Peptide Groups: For peptide group data.

X Data

Specifies a principal component.

Y Data

Specifies a principal component.

Center and Scale

Mean-centers the values in a covariance matrix. If you clear this checkbox, the chart uses the original values in the covariance matrix.

Use Normalized Abundances

Displays normalized abundance values in the chart.

The Use Normalized Abundances checkbox, selected by default, is only available when you normalize the data with the normalization parameters of the Reporter Ions Quantifier node or the Precursor Ions Quantifier node in the consensus workflow. If you clear this checkbox, the chart uses abundance values that are not normalized.

Legend

Displays the group colors.

Default: Hidden (Select Show Legend from the shortcut menu to display the legend.)

Scores Plot page

 

Circles

Represent samples as data points.

When you select the Show Position ToolTips command, pointing to a data point displays the following information:

  • number: The sample number.
  • Sample: The data point is a sample.
  • Replicate number: The number of the replicate.
  • number, number: The coordinates of the data point on the plot.

x-axis

Displays the principal component that you selected in the X Data box.

y-axis

Displays the principal component that you selected in the Y Data box.

Loadings Plot page

 

Circles

Represent individual proteins as data points.

When you select the Show Position ToolTips command, pointing to a data point circle displays the following information:

  • number, number: The coordinates of the data point on the plot.
  • Accession_number: The accession number.
  • MW number [kDA]=number: The calculated molecular weight of the protein, in kilodaltons.
  • Calc pI=number: The theoretically calculated isoelectric point for the protein, which is the pH at which a particular molecule carries no net electrical charge.
  • # Peptides=number: The number of distinct peptide sequences in the protein.
  • # PSMs=number: The number of identified peptide spectrum matches identified from all included searches, including those redundantly identified.
  • #AAs=number: The length of the protein sequence.

x-axis

Displays the values that you selected in the X Data box.

y-axis

Displays the values that you selected in the Y Data box.

Variances Plot page

 

Circles

Displays the proportion of variance.

Squares

Displays the cumulative proportion of variance.

# PC (x-axis)

Displays the number of principal components.

Proportion of Variance (y-axis)

Displays the proportion and the cumulative proportion of the variance contributed by each principal component.