RTAnnotator

Adds RT information to identifications in mzid.

pot. predecessor tools	$\longrightarrow$ QCCalculator $\longrightarrow$	pot. successor tools
XTandemAdapter		MascotAdapterOnline
IDFilter		QCCalculator

RT is no mandatory attribute in a PSM representation of MzIdentML. Some identification engines do omit this information. Though, as the RT will be crucial for further analyses, all (e.g. ) reading MzIdentML will warn you about missing RT. This tool performs the annotation of the identification given the source file to the identification process.

Note

For mzid in-/out- put, due to legacy reason issues you are temporarily asked to use IDFileConverter as a wrapper. The command line parameters of this tool are:

RTAnnotator -- Annotates identification files that are missing the RT field
Version: 2.0.0 May 16 2015, 09:22:21, Revision: GIT-NOTFOUND

Usage:
  RTAnnotator <options>

Options (mandatory options marked with '*'):
  -in_msref <file>*  Mass spectra file as reference input for RT lookup (valid formats: 'mzML')
  -in <file>*        Identifications without RT field (valid formats: 'mzid', 'idXML')
  -out <file>*       Output file (identifications). (valid formats: 'mzid', 'idXML')
                     
Common UTIL options:
  -ini <file>        Use the given TOPP INI file
  -threads <n>       Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>  Writes the default configuration file
  --help             Shows options
  --helphelp         Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+RTAnnotatorAnnotates identification files that are missing the RT field

version2.0.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'RTAnnotator'

in_msref Mass spectra file as reference input for RT lookupinput file*.mzML

in Identifications without RT fieldinput file*.mzid,*.idXML

out Output file (identifications).output file*.mzid,*.idXML

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

forcefalse Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false