Export annotated spectra - Proteome Discoverer Software - Export annotated spectra - Proteome Discoverer Software - Proteome Discoverer Software

Procedure

1. Open your search results in the result file. See Organizing results.
2. Choose File > Export > Annotated Spectra.
3. The Export Annotated Spectra dialog box open.

4. 

3. In the Destination Folder box, do one of the following:
1. Type the path and name of the ZIP file where you want to store the image and the TXT file for the annotated peptides.
2. –or–
1. Locate and select the ZIP file (or type the name of the ZIP file where you want to store the image and the TXT file for the annotated peptides), and then click Save in the Save As dialog box.
4. In the Items To Be Exported area, select the check boxes corresponding to the type of spectra that you want to export:
1. From PSMs: Exports the annotated spectra of the PSMs.
2. From Peptide Groups: Exports the annotated spectra of all PSMs for all peptide groups. This option is only available if the result file includes peptide groups.
3. From Proteins: Exports all PSMs of the proteins.
5. To export only certain spectra in the categories that you selected in the Items To Be Exported area, do the following:
1. On the appropriate page of the result file, select the check box to the left of each item that you want to export. For information on selecting these check boxes, see Check items on the pages of a result file.
2. In the Items To Be Exported area of the Export Spectra dialog box, select the Checked Items Only check box.
3. If you do not select the Checked Items Only check box, the application exports all spectra in the categories that you selected.
6. In the Options/Image Size area, specify the width and height of the spectra.
1. Width: Specifies the width of the spectra, in centimeters. The default is 16.00 centimeters.
2. Height: Specifies the height of the spectra, in centimeters. The default is 8.00 centimeters.
7. Click Fragment Match Options.
8. The Fragment Match Options dialog box open.

9. 

10. For parameter information, see Fragment match options page parameters.
8. Do the following in the Fragment Match Options dialog box:
1. To load the most recently saved settings, click Load.
2. Select a state from the Charge Detail Level list from the following settings:
1. (Default) All: Displays all fragment ions, regardless of charge.
2. +1: Displays singly charged fragment ions.
3. +2: Displays doubly charged fragment ions.
4. +3: Displays triply charged fragment ions.
5. +4, +5, +6, +7: Displays additional charged fragment ions if available.
3. In the Annotation Threshold area, specify a peak intensity limit from either of these methods:
1. (Default) % of Base Peak: Specifies an intensity threshold as a percentage of the base peak in the spectrum. The base peak is the largest peak in a spectrum.
2. Absolute: Specifies an absolute intensity threshold.
3. Peaks below the limit are not annotated. This limit prevents the addition of too many labels to a spectrum, especially if the low-intensity peaks are noise peaks.
4. When you want colored lines denoting a, b, and y ions to appear at the bottom of each spectrum image, select the Show Legend check box.
5. The Show Reference Spectrum check box
6. To use the match tolerances and ion series set for the search node, select the Use Search Settings check box.
7. In the Match Tolerances area, select the type of mass analyzer that was used to obtain the spectrum.
8. Specify the match tolerance. The application annotates the spectrum with ions that it assigns within this mass tolerance. You can use daltons (Da) or parts per million (PPM).
9. In the Fragments area, select the type of fragment ions to include in the annotated exported spectra:
   - Select the activation type from the Activation Type list.
   - Select the check boxes corresponding to the fragment ion type.
10. To save the settings as the default settings, click Save at the top of the dialog box.
11. Click OK to apply the settings and close the Fragment Match Options dialog box.
9. In the Export Annotated Spectra dialog box, click Export, or to cancel this operation and any changes you made, click Close.
10. If you click Export, a meter in the lower left corner of the Export Annotated Spectra dialog box indicates the progress of the exportation.
10. When you receive a message that the export job is finished, click OK.