The Grouping & Quantification page - Proteome Discoverer Software - The Grouping & Quantification page - Proteome Discoverer Software - Proteome Discoverer Software

1

Generated Sample Groups area: Displays samples grouped by the values set for the selected study factors. Selecting these variables indicates that you want to group your samples and quantification ratios according to the specified study variables. The grouping of samples affects how identifications are displayed in the distribution maps and the calculation of quantification results. For the latter, the application reports separate area values for each sample or sample group. If the application does not use all available sample group values in at least one ratio, it displays a warning in the Generated Sample Groups area.

2

Generated Ratios area: Displays the ratios generated.

3

Bulk Ratio Generation area: Displays the study factor values to use as the denominators for multiple generating groups of quantification ratios.

4

Manual Ratio Generation area: Contains menus where you can select the numerator and denominator for each quantification ratio.

5

Study Variables area: Contains a list of the selectable study factors, or study variables, that you specified in the Study Factors area of the Study Definition page. In this area, you can select the study factors that you want to use to sort samples and quantification ratios into replicate groups and treatment groups.

• Files: Groups samples and quantification ratios by files.
• Quan Channel: Groups samples and quantification ratios by quantification channels.
• Study_factors: Groups samples and quantification ratios by userdefined study factors.
• Sample Types: Groups factors that include Sample and Control. Variables displayed in italics contain only a single value.