tide-search

Usage:

./tide-search [options] --peptides=<filename> --proteins=<filename> --spectra=<filename> > results

Description:

The tide-search program searches for matches between observed tandem mass spectra and peptides from the given peptide and protein databases.

Input:

• A protein index, created using tide-index. The protein index file name is set using --proteins=<filename>.
• A peptide index, created using tide-index. The peptide index file name is set using --peptides=<filename>.
• A file of spectra, created using msconvert. The spectra file name is set using --spectra=<filename>.

Output:

A list of peptide-spectrum matches is generated.

• If the --results=text option is specified (default), the matches are written to standard output. If the --results=protobuf option is specified, the matches are written to a binary file to be viewed later using tide-results.

Options:

• --mass_window=<float>   Specify the precursor mass tolerance in Daltons. Default=3.
• --top_matches=<integer>   Specify the number of matches to report for each spectrum. Default=5.
• --results=text|protobuf   Specify whether output should be in text format or binary (protobuf) format. The protobuf format is readable by the included tide-results program, which can display results in several formats.

Example

./tide-search --peptides=yeast.fasta.pepix --proteins=yeast.fasta.protix --spectra=yeast-02-10000.spectrumrecords > results