OpenMS
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Can be used to calibrate the RTs of peptide hits linearly to standards.
pot. predecessor tools | → IDRTCalibration → | pot. successor tools |
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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 -- Calibrate RTs of peptide hits linearly to standards. Full documentation: http://www.openms.de/doxygen/release/3.3.0/html/TOPP_IDRTCalibration.html Version: 3.3.0 Dec 21 2024, 15:25:20, Revision: 35c5e65 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: