Parameters in the Sample Abundances view - Proteome Discoverer Software - Parameters in the Sample Abundances view - Proteome Discoverer Software - Proteome Discoverer Software

Color 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.

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).

Data Source

Specifies the result category to plot the data from:

• Proteins: Plots from protein data.
• Peptide Groups: Plots from peptide group data.

Transform Data

Determines whether the data appears in a linear scale or the log₁₀ scale.

Selecting this checkbox transforms the area counts to the log₁₀ scale.

Use Normalized Areas

Displays normalized chromatographic peak areas.

The checkbox is available if the Reporter Ions Quantifier node or the Precursor Ions Quantifier node normalized the quantification data, but did not scale it.

Graph

Groups (x axis)

Displays the name of the sample groups.

LogArea/Area (10⁹) (y axis)

Displays the area in a linear scale or in a log₁₀ scale, depending on the setting of the Log-Transform Data parameter.

• LogArea: Displays the peak area in log₁₀ scale.
• Area (10⁹): Displays the peak area in linear scale.

Rectangles

The rectangles represent the second and third quartiles for the data set.

When you choose the Show Position tooltips command, placing the cursor over the rectangle displays the following information:

• Name: The name of the raw data file that the sample group belongs to.
• Group: The name of the sample group.
• Max: The maximum value of the chromatographic peak area within the sample group, including the outliers.
• 3rd Q: The third quartile of the chromatographic peak area within the sample group.
• Median: The median of the chromatographic peak area within the sample group.
• Mean: The mean of the chromatographic peak area within the group.
• 1st Q: The first quartile the chromatographic peak area within the sample group.
• Min: The minimum value of the chromatographic peak area within the sample group, including the outliers.
• StdDev: The standard deviation of the chromatographic peak area within the sample group.

Circles

Represent outlier data points.

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

• Accession_number: The accession number.
• MW number [kDA]=number: The calculated molecular weight of the protein.
• Calc pI=number: The theoretically calculated isoelectric point for the protein—that 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.

Legend

Displays the group colors.

By default, the legend is hidden. Choose Show Legend from the shortcut menu to display it.