Creating a peptide index

The search for peptide-spectrum matches requires looking through all possible peptides in the protein database (fasta file). A text file in fasta format is not well-suited for this task, so crux can create an index to speed up the process. To create an index for the fasta file used in the search example, run this command.


crux create-index small-yeast.fasta yeast-index

The output should look like this

INFO: Using amino acid alphabet (ACDEFGHIKLMNPQRSTVWYBUXZ).
INFO: Total proteins found: 56
INFO: reached peptide 1000
INFO: Printing index
INFO: Sorting index
INFO: crux-create-index finished.

Once the index is created, you will see that there is a new directory called yeast-index. In this directory are many files with names beginning with crux_index_ followed by a number. Each of these binary files contains one portion of the index. The remaining binary file, small-yeast_binary_fasta, contains the peptides that the index is referencing.

Note: The index was created with the default parameter settings, all of which can be changed in a parameter file or on the command line. See Customizing a Search for details.

The text file crux_index_map lists the masses contained within each index file. The other text file, README, describes all of the parameters used in creating the index. README should look like this.

#       time created: Mon Jan 28 14:02:29 2008
#       fasta file: small-yeast-binary-fasta 
#       min_mass: 200.00
#       max_mass: 7200.00
#       min_length: 6
#       max_length: 50
#       peptide_type: tryptic
#       missed_cleavage: false
#       mass_type: average
#       unique peptides: redundant
#       CRUX index directory: yeast-index
#       target mass range for index file: 6.84

Using an index

The index you have created can be used when searching for peptide-spectrum matches and in the subsequent analysis of matches. Try a search with demo.ms2 (also found in the test data) with the indexed protein database. Run these commands.


$ crux search-for-matches demo.ms2 yeast-index

$ crux percolator yeast-index

The next section will discuss other crux options and how to set them.