Use the Method Editor for precursor ion quantification - Proteome Discoverer Software - Use the Method Editor for precursor ion quantification - Proteome Discoverer Software - Proteome Discoverer Software

Prerequisites

1. You have the Quantification Method Editor dialog box open. See Create a quantification method.

Procedure

1. For in vivo metabolic quan labeling (for example, SILAC), clear the Quan Labels Themselves are Modifications on a Side Chain or the N-Terminus checkbox.

2. NOTE

   By default, this checkbox is selected. Select this checkbox for dimethylation, and clear it for SILAC modifications.

2. In the quantification channel box (far left), select the name of the labeling method to use:
1. Heavy: Refers to amino acid labels that use heavy isotopes, for example, Arg10 and Lys8.
2. Medium(3plex methods only): Refers to amino acid labels that use less massive isotopes, for example, Arg6 and Lys4.
3. Light: Refers to amino acid labels that use normal isotopes.
3. To add a quantification channel, select the plus button (+) below the list of quantification channels on the left.
4. The new channel is added to the list on the left of the dialog box, and the following default name appears in the Channel Name box: New number.

5. 

4. To remove a quantification channel, select the quantification channel from the list on the left and select the minus button (–) below the list.
5. To specify a name for the new quantification channel, delete the default name in the Channel Name box and then enter the new name.
6. The new name appears in the quantification channel list.
6. To specify a quantification label to assign to a quantification channel, select the plus button (+) below the Quantification Labels box.
7. A default quantification label (New number) appears in the Quantification Labels box and the Label Name box.
7. To remove an existing quantification label, select the label in the Quantification Labels box and select the minus button (–) below it.
8. To change the default quantification channel name, delete the old name in the Label Name box and then enter the new Label Name. The following example uses: Arg6, Lys6.
9. In the Modification Target area, select the location of the label on the peptide from the following options:
1. Side Chain Modification: The label occurs on a side chain.
2. N-Terminal Modification: The label occurs on the N terminus.
3. C-Terminal Modification: The label occurs on the C terminus.
10. From the Modification dropdown list, select the modification for the amino acid label.
11. From the list next to the Modification list, select the abbreviation of the amino acid selected in the Quantification Labels box that the modification occurs on.

12. 

12. When you finish setting the parameters in the Quantification Method Editor, select OK.
13. The Save Quantification Method dialog box opens.
13. In the Save as New Method box, enter the name of the new method.
14. Select Save.
15. The new quantification method appears in the Quantification Methods view.