You can create a predicted spectrum library to use with the MSPepSearch node.

NOTE

Ensure that you have sufficient disk space for the predicted library.

For example, the human proteome trypsin digest (when using typical settings) produces about 10,000,000 peptide tandem mass spectra. The associated library creation requires 100 GB, of which 50 GB are used to store the library.

If the current drive does not have enough space for spectral libraries, you can change the location. For more information, see Change the location of the spectral library files.

NOTE

Each spectrum is approximately 5 KB.

Procedure

  1. Select Administration > Maintain Spectrum Libraries.
  2. Select Predict.
  3. In the Predict a Spectrum Library dialog box, under General, do the following:
  4. Select a FASTA file.
  5. The dropdown list contains all the FASTA files available. To add more, see Managing FASTA indexes.
  6. For Library Name, enter a name.
  7. For Activation Type, select HCD or CID.
  8. For Collision Energy, enter the value that matches the data being searched.
  9. (Optional) Enter a comment.
  10. Under Digest, enter a number for the following parameters:
  11. Min. Peptide Length (Range: 7–30; default: 7)
  12. Max. Peptide Length (Range: 7–30 default: 7)
  13. Min. Precursor Charge (Range: 1–6; default: 2)
  14. Max. Precursor Charge (Range: 1–6; default: 3)
  15. Maximum Missed Cleavage (Range: 0–12; default: 2)
  16. For Static Modification dropdown list, select the modification.
  17. For Dynamic Modification dropdown list, select the modification.
  18. For Max. Equal Modifications Per Peptide, enter a number or keep the default value.
  19. Select Start.