The following table describes the parameters in the FASTA Index Creator dialog box.

FASTA Index Creator dialog box parameters

Parameters

Description

General

Sets general options for the creation of the FASTA index.

Auto Remove

Specifies whether the available FASTA indexes are removed from memory after the number of indexes reaches the specified maximum. The options are as follows:

  • (Default) True: Automatically removes the FASTA indexes from memory.
  • False: Keeps the FASTA indexes in memory.

Create Additional Decoy Database Index

Determines whether the application creates an index for the specified FASTA file and an index for the decoy version of the FASTA file. The options are as follows:

  • True: Creates an index for the specified FASTA file and an index for the decoy version of the FASTA file.
  • (Default) False: Does not create an index for the specified FASTA file nor an index for the decoy version of the FASTA file.

Input Data

Specifies the basic information that the application requires to create the index.

FASTA File

Specifies the name of the FASTA database.

Enzyme Name

Specifies the name of the enzyme used for digestion and the type of digestion. The type of digestion is listed in parentheses after the enzyme name, and can be one of these options:

  • Full: Specifies a full enzymatic digestion.
  • Semi: Specifies a semi-enzymatic digestion.
  • Unspecific: Specifies a non-specific digestion.
  • No Cleavages: Specifies that no cleavages occur.

Maximum Missed Cleavage Sites

Specifies the maximum number of internal cleavage sites (per peptide fragment) that an enzyme is allowed to miss when cleaving peptides during digestion.

Range: 0–12; default: 2

Mass Range Settings

Sets the limits of the mass range of the singly charged precursor ion to be processed.

Minimum Precursor Mass

Specifies the minimum mass of the precursor ion.

Minimum: 0.0 Da; maximum: 10 000.0 Da; default: 350 Da

Maximum Precursor Mass

Specifies the maximum mass of the precursor ion.

Range: 0.0–10 000.0 Da; default: 5000 Da

Use Average Precursor Mass

Determines whether the average mass is used to match the precursor ion. The options are as follows:

  • 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.

Static Modifications

Specifies the static modifications that occur on the amino acid.

Peptide N-Terminus

Specifies the static modification that occurs on the N-terminus of the peptide.

Peptide C-Terminus

Specifies the static modification that occurs on the C-terminus of the peptide.

Static Modification boxes

Specifies the static modification that occurs anywhere on the amino acid side chain.