Before performing the search, you can determine whether the XlinkX algorithm retains or discards the FASTA file index created during processing. Retaining the FASTA file index generated during processing can save time during future processing but requires significant disc space. The storage location is:

C:\ProgramData\Thermo\Proteome Discoverer 3.1\FastaDatabases\hlxl_indices

Procedure

  1. Select Administration > Configuration.
  2. In the Configuration pane, select XlinkX/PD Search.
  3. The General Data area appears on the Administration page.
  5. On the Retain FASTA File Indexes line, select one of the following settings:
  6. True: Uses the FASTA file index generated during previous processing.
  7. False: Regenerates the FASTA file index.