To use a spectrum library, the application must register it. If you have a local spectrum library that you did not download directly into the application, you must import the library by using the Add button. During registration, the application:

  • Transfers the file or archives it to the server
  • Converts the library to an internal format, which includes the following:
    • Extracting the library spectrum and peptide match annotations
    • Annotating the library spectrum with the activation type and fragment match tolerance specified when the library was added
    • Mapping modifications to known modifications
  • Registers optional FASTA files contained in the library archive and generates mapping from the peptide matches in the library to the proteins in the FASTA file.
  • Generates the target and decoy versions of the library in MSPepSearch binary format.

For information on downloading a ready-to-use spectrum library directly into the application, see Download a spectrum library.

Procedure

  1. Outside of the Proteome Discoverer application, download the appropriate spectrum libraries from the National Institute of Standards and Technology (NIST) at http://peptide.nist.gov or from Peptide Atlas at http://www.peptideatlas.org/speclib.
  2. In the application, select Administration > Maintain Spectrum Libraries.
  3. Select Add.
  4. In the Spectrum Library Import dialog box, do the following:
  5. For Library File, select the file selector icon, and select the spectrum library file.
  6. Select Open.
  7. The Spectrum Library Import dialog box opens.
  8. For Library Name, enter a name, or accept the default (that is, the entry for Library Name without the suffix).
  9. (Optional) Enter a number for Version.
  10. (Optional) Enter a description for Organism.
  11. Select the activation type from the Activation Type dropdown list..
  12. The activation type determines the fragment ion types used for annotating the fragment peaks in the library spectra.
  13. For Fragment Match Tolerance, enter a number and select the corresponding unit, Da or ppm.
  14. This value is used for annotating the fragment peaks in the library spectra.
  15. (Optional) For Collision Energy (Min-Max), enter a value for one or both fields.
  16. (Optional) Enter a comment.
  17. Adding a Spectral Library
    Adding a Spectral Library
  18. Select OK.
  19. The job queue in the Administration view displays the status each step of library creation. When the application finishes adding the spectrum library, it appears in the Spectrum Libraries view.
  20. If the application finds unknown modifications, you must manually map them before you can search the library or export it. See Map unrecognized modifications.