The ProSightPD application installs with a database and analysis workflow template for the Thermo Scientific™ Pierce™ Intact Protein Standard Mix. You can download an example of the Pierce Intact Protein Standard Mix data file at the Life Sciences Mass Spectrometry Software Download and Licensing Portal.

The Pierce Intact Protein Standard Mix contains six recombinant proteins. For additional information, refer to https://www.thermofisher.com/order/catalog/product/A33527#/A33527. This data file was collected on a Thermo Fisher Scientific Fusion Lumos Tribrid Mass Spectrometer with high resolution precursor and HCD fragment ions scans.

To become familiar with the ProSightPD data analysis process using example data, complete the following steps.

Procedure

  1. Download the Pierce_Intact_Protein_Standard_Top_Down_Example.raw data file at the Life Sciences Mass Spectrometry Software Download and Licensing Portal.
  2. Open the Proteome Discoverer application.
  3. On the Start page, select New Study/Analysis.
  4. The New Study and Analysis dialog box opens.
  5. Enter the Study Name.
  6. For the Study Root Directory, select the browse icon and locate the path.
  7. Select OK.
  8. The study opens.
  9. Select Open Analysis Template and locate the PSPD HiHi TopDownStandard Analysis Template (C:\Users\Public\Documents\Thermo\Proteome Discoverer 3.2\Common Templates\ProSightPD 4.4\Analysis Templates).
  10. Select Open.
  11. Select the Workflows tab on the Study page.
  12. In the Processing Step area of the Analysis pane, select Edit.
  13. In the Workflow Tree, select the Annotated Proteoform Search node.
  14. In the Parameters of the ‘ProSightPD 4.4 Annotated Proteoform Search’ area on the left side of the Workflow Tree, select the Input Database dropdown arrow and select the PierceIntactProteinStandardMix database file (it is the only database available for newly installed software).
  15. Repeat step 12 for the second Annotated Proteoform search node and the Subsequence Search node and change the Input Database to the PierceIntactProteinStandardMix database file.
  16. Select the Input Files tab on the Study page.
  17. Select Add Files.
  18. The Add Files dialog box opens.
  19. Locate the Pierce_Intact_Protein_Standard_Top_Down_Example.raw data file that you downloaded at the beginning of this process, then select Open.
  20. The file is now listed on the Input Files page.
  21. Drag and drop the file into the Processing Step area of the Analysis pane on the right side.
  22. The Run button now activates and turns green.
  23. Select Run.
  24. After you select Run, the Administration page automatically opens where you can monitor the progress of your analysis. For additional information about viewing your results, see Working with results.