A FASTA index is a type of lookup table containing masses, theoretical peptide sequences, and associated proteins, which minimizes search time. The index lists all possible amino acid sequences that can be produced when an enzyme digests a protein or peptide. The peptide fragments are listed by molecular weight. The index stores information about every nominal mass, every peptide that has that mass, every protein that contains this peptide, and the location of its protein description in the FASTA file.
Rather than read all protein sequences from the FASTA file, digest them in silico with the specified enzyme, calculate the mass of each peptide, and compare it to the given precursor mass, the Proteome Discoverer application looks for the specific mass in the FASTA index and uses it to find both the peptides that have this mass and the associated proteins that contain the peptides.
For full enzymatic searches, the application automatically creates FASTA indexes as they are needed. It does not automatically create FASTA indexes during semi-enzymatic or no-enzyme searches because these searches usually consume a large amount of space on a computer’s hard drive. However, you can manually create FASTA indexes for these types of searches.