Generate custom quantification ratios semiautomatically - Proteome Discoverer Software - Generate custom quantification ratios semiautomatically - Proteome Discoverer Software - Proteome Discoverer Software

Procedure

1. In the Study Variables area of the Grouping & Quantification page, select the checkboxes of the study variables that you want to use to group your samples and choose ratios.
2. After you select the study factors, the Generated Sample Groups area displays the updates.
3. This step creates sample groups using the selectable study factors available for the files to be analyzed. The application places all samples that have the same combination of study factor values in the same group.

4. NOTE

   The order of the study factors is relevant for the semiautomatic generation of ratios.

2. (Optional) To change the placement of a study factor in the list of study factors, do the following:
1. In the Study Variables area, select the checkbox of the study factor that you want to move.
2. A placement handle appears to the left of the selected checkbox.

3. 

2. Point to the placement handle.
3. White up and down arrows appear on the handle.
3. Do one of the following:
   - Drag the cursor up or down to move the variable to its new place in the list of variables.
   - Select the up or down arrows to move the study factor.
3. (Optional) To sort both the study factors in the Bulk Ratio Generation area and the sample groups in the Generated Sample Groups area, do either of the following:
1. To sort these items in descending order, select the Sort Descending .
2. To sort these items in ascending order, select the Sort Ascending .
4. In the Bulk Ratio Generation area, select the checkbox for the sample group that you want to use in the denominator of the ratio.
5. (Optional) If you selected more than one study factor, you can use the same study factor for all denominators as follows:
1. Point to a denominator value.
2. An icon containing four checkboxes in a square appears on the left side of that item.
2. Select the icon, .
3. The application uses the selected study factor for all denominators.

4. 

6. Select Add Ratios.
7. The application generates all possible ratios against the selected denominator values and adds them to the Generated Ratios area. See the following figure.