IDRTCalibration

Can be used to calibrate the RTs of peptide hits linearly to standards.

pot. predecessor tools	→ IDRTCalibration →	pot. successor tools
MascotAdapter (or other ID engines)		PeptideIndexer (or other tools operating with identifications (in idXML format))

This tool can be used to linearly align RTs of the idXML-File to a reference. If only calibrant_1_input and calibrant_2_input are given, the first calibrant will result at RT 0.1 and calibrant_2_input will be at 0.9. If one wants to align the RTs of this idXML file to the IDs of a reference file one can also give the RTs of the same calibrant in the reference file (calibrant_1_reference, calibrant_2_reference). If these calibrants are given, the linear transformation (shift and scale) will be calculated such that calibrant_1_input will be at the same RT as calibrant_1_reference and calibrant_2_input will be at the same RT as calibrant_2_reference. This only applies if calibrant_1* has a smaller RT than calibrant_2*. Otherwise the values are swapped.

Note

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

IDRTCalibration -- Calibrate RTs of peptide hits linearly to standards.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_IDRTCalibration.html
Version: 3.3.0-pre-nightly-2024-11-20 Nov 21 2024, 02:34:56, Revision: decb5c8
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  IDRTCalibration <options>

Options (mandatory options marked with '*'):
  -in <file>*                  Input file  (valid formats: 'idXML')
  -out <file>*                 Output file  (valid formats: 'idXML')
  -calibrant_1_reference <RT>  The RT of the first calibrant in the reference file. (default: '0.1')
  -calibrant_2_reference <RT>  The RT of the second calibrant in the reference file. (default: '0.9')
  -calibrant_1_input <RT>      The RT of the first calibrant in the input file. Please note that this value 
                               needs to be set. The default value -1.0 is not allowed. (default: '-1.0')
  -calibrant_2_input <RT>      The RT of the second calibrant in the input file. Please note that this value 
                               needs to be set. The default value -1.0 is not allowed. (default: '-1.0')
                               
Common TOPP 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

+IDRTCalibrationCalibrate RTs of peptide hits linearly to standards.

version3.3.0-pre-nightly-2024-11-20 Version of the tool that generated this parameters file.

++1Instance '1' section for 'IDRTCalibration'

in input file input file*.idXML

out output file output file*.idXML

calibrant_1_reference0.1 The RT of the first calibrant in the reference file.

calibrant_2_reference0.9 The RT of the second calibrant in the reference file.

calibrant_1_input-1.0 The RT of the first calibrant in the input file. Please note that this value needs to be set. The default value -1.0 is not allowed.

calibrant_2_input-1.0 The RT of the second calibrant in the input file. Please note that this value needs to be set. The default value -1.0 is not allowed.

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 Overrides tool-specific checkstrue, false

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