Procedure

  1. Open a workflow template that includes the ProSightPD Single Proteoform Search node, or add the node after the cRAWler node.
  2. In a web browser, navigate to https://proteininformationresource.org/cgi-bin/resid.pl.
  3. Note the modification ID from the database of choice.
  4. In the Proteome Discoverer application, select the ProSightPD Single Proteoform Search node, and then select Advanced Parameters.
  5. In the Proforma Sequence, enter the protein sequence as shown in the following figure.
  6. The Proforma Sequence is the protein sequence plus the modification in the form of a Proforma database entry. Enter the modification number after the residue to be modified in brackets.
  7. NOTE

    Put the identifier in brackets after the amino acid containing the modification. For example, AA0057 N2-acetyl-L-lysine becomes AA0057, and an acetylation of a lysine residue in a protein sequence is expressed as [AA0057].

  8. To add the modification, enter the modification number in brackets after the residue.
  9. For manual precursor mass assignment, in the crawler node’s Advanced Parameters, do the following:
  10. Set Use Manual Precursor to Always or If Not Detected.
  11. Enter the expected Precursor Mass (Daltons).
  12. Configure the consensus workflow, or select Run.
  13. For basic workflow information, refer to the Proteome Discoverer User Guide.

For more information about using the node, see Single Proteoform Search node.