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.
The command line parameters of this tool are:
IDRTCalibration -- Can be used to calibrate RTs of peptide hits linearly to standards.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
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')
-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')
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:
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |