Practical report format

URL Value Description sort   startup Sort table of peptides by ascending start residue number, (default) massup Sort table of peptides by ascending mass massdown Sort table of peptides by descending mass showall   true Show all calculated peptides, not just matched peptides false Show just matched peptides, (default) _showallfromerrortolerant ShowAllFromErrorTolerant 1 Set value to 1 to report all matches from an error tolerant search, including the garbage, (default 0) _onlyerrortolerant   1 Set value to 1 to report only error tolerant matches from an automatic error tolerant search, (default 0) _noerrortolerant   1 Set value to 1 to suppress error tolerant matches from an automatic error tolerant search, (default 0) _show_decoy_report   1 Set value to 1 to display the report for an automatic decoy database search, (default 0) _sigthreshold SigThreshold N Probability to use for the significance threshold. Range is to 1E-18. Default is . _ignoreionsscorebelow IgnoreIonsScoreBelow N Values greater than 0 and less than 1 act as an expect value threshold, and the scores for any peptide matches with higher expect values are set to 0, so that they disappear from the report. Values of 1 or more act as a score threshold, and any peptide matches with lower scores suppressed. Floating point number, (default ). _server_mudpit_switch MudpitSwitch N Protein score calculation switches to large search mode when the ratio between the number of queries and the number of database entries, (after any taxonomy filter), exceeds this value, (default ). _featuretablelength FeatureTableLength N Length of database entry in bases at which protein view switches to GenBank output. Default 30000 _featuretableminscore FeatureTableMinScore N Score threshold for inclusion in GenBank feature table format, if undefined then report includes matches that exceed lower of homology or identity threshold indyenzyme   N If enzyme was independent, display cleavage products for this specificity index frame   N For a nucleic acid database, display matches in this frame number percolate Percolator 1 Set value to 1 to re-rank results using Percolator, (default 0). percolate_rt PercolatorUseRT 1 Set value to 1 to include retention time feature when using Percolator, (default 0).

Practical report format

practical report format

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