tide-results

Usage:

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

Description:

The tide-results program displays Tide search results as computed by tide-search. Several display formats are available. The search step is to have been previously performed by tide-search, and the result file is to have been saved in protobuf format using the --results=protobuf command-line switch. The spectrum file (.spectrumrecords file suffix) and the protein index (.protix file suffix) used during the search must also be available.

Input:

• A results file generated during tide-search. This are the search results to display. The file name is set using: --results_file=<filename>.
• The protein index used during tide-search. The protein index file name is set using --proteins=<filename>.
• The file of spectra used during tide-search. The spectra file name is set using --spectra=<filename>.
• --aux_locations=<filename>. File of auxiliary locations created by tide-index during the indexing process. This file is required only if the --show_all_proteins option (described below) is specified, and may be omitted otherwise.

Output:

• A list of peptide-spectrum matches is written to a specifiable output file in one of three formats.

Options:

• --out_filename=<filename> – Name of the output file to generate. If omitted, a default output filename will be generated using the specified input file name and output format.
• --show_all_proteins=<string> – Display all the proteins the peptide was found in. Requires the --aux_locations flag to be set (see above).
• --show_mods=<string> – Display modifications in the peptide sequence.
• --out_format=<string> – The output format to be generated. Can be text, pep.xml or sqt. Default is text.

Detailed output formatting options. The following options allow detailed specification of what information to display for each search result.

• --spectrum_fields=<string> – A comma delimited set of fields to show for an experimental spectrum in the order listed. Available options are: spectrum_num,mz,charge. Default: spectrum_num,mz,charge
• --match_fields=<string> – A comma delimited set of fields to show for a matching peptide in the order listed. Available options are: xcorr,sequence. Default: xcorr,sequence
• --protein_fields=<string> – (A comma delimited set of fields to show for a protein associated with a matching peptide. Available options are: protein_name,pos,aa_before,aa_after. Default: protein_name,pos,aa_before,aa_after

Example

./tide-results --results_file=yeast.results --proteins=yeast.fasta.protix --spectra=yeast-02-10000.spectrumrecords --out_filename=yeast.results.text --out_format=text