Manually create a FASTA index - Proteome Discoverer Software - Manually create a FASTA index - Proteome Discoverer Software - Proteome Discoverer Software

Procedure

1. Select Administration > Maintain FASTA Indexes.
2. Select Add.
3. The FASTA Index Creator dialog box opens.
3. In the General area, specify whether the application removes the available FASTA indexes from memory after the number of indexes reaches the specified maximum.
1. True (Default): Automatically removes the FASTA indexes from memory
2. False: Keeps the FASTA indexes in memory.
3. For information about how the application removes FASTA indexes after the maximum has been reached, see Control automatic FASTA index removal. For instructions on specifying the maximum number of indexes, see Change the number and location of stored FASTA indexes.
4. In the Input Data area, specify the basic information that the application requires to create the index:
1. FASTA File: Select the FASTA database to be indexed from the list.
2. Enzyme Name: Select the enzyme used in the digestion from the list on the left (the enzymes on this list are set in the Cleavage Reagents window) and select the type of digestion from the list on the right:
   - Full: Specifies a full enzymatic digestion.
   - Semi: Specifies semi-enzymatic digestion.
   - Unspecific: Specifies a non-specific digestion.
   - No Cleavages: Specifies that no cleavages occur.
3. Maximum Missed Cleavage Sites: Specifies the maximum number of internal cleavage sites per peptide fragment that is acceptable for an enzyme to miss when cleaving peptides during digestion. Normally, the digestion time is too short to enable the enzyme to cleave the peptide at all positions, so you must specify the number of missed positions in one resulting peptide fragment where the enzyme could cleave but did not.
4. Minimum: 0; maximum: 12; default: 2
5. In the Mass Range Settings area, set the limits of the mass range of the singly charged precursor ion to be processed:
1. Minimum Precursor Mass: Specifies the minimum mass of the precursor ion.
2. Minimum: 0.0 Da; maximum: 10 000.0 Da; default: 350 Da
1. Maximum Precursor Mass: Specifies the maximum mass of the precursor ion.
2. Minimum: 0.0 Da; maximum: 10 000.0 Da; default: 5000 Da
1. Use Average Precursor Mass: Determines whether the average mass is used to match the precursor ion.
   - True: Uses the average mass to match the precursor ion.
   - False (Default): Uses the monoisotopic mass to match the precursor ion, which is the mass of the most abundant isotope of the protein, peptide, or fragment ion.
6. In the Static Modifications area, specify the static modifications that occur on the amino acid:
1. Peptide N-Terminus: Select the static modification that occurs on the N terminus of the peptide.
2. Peptide C-Terminus: Select the static modification that occurs on the C terminus of the peptide.
3. Static Modification: Select the static modification that occurs on the amino acid side chain.
7. Select Start.
8. The application starts creating the FASTA index, and the job queue appears.

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8. When the job finishes, select Administration > Maintain FASTA Indexes to display the FASTA Indexes view.
9. Select Refresh.
10. The new FASTA index appears in the FASTA Indexes view on the Administration page. The application creates an index for the specified FASTA file and the decoy version of the FASTA file.

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