OpenMS
2.6.0
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Converts different spectral libraries / transition files for targeted proteomics and metabolomics analysis.
Can convert multiple formats to and from TraML (standardized transition format). The following formats are supported:
The command line parameters of this tool are:
TargetedFileConverter -- Converts different transition files for targeted proteomics / metabolomics analysis. Full documentation: http://www.openms.de/documentation/UTILS_TargetedFileConverter.html Version: 2.6.0 Sep 30 2020, 12:54:34, Revision: c26f752 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. Usage: TargetedFileConverter <options> This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript ion or use the --helphelp option. Options (mandatory options marked with '*'): -in <file>* Input file to convert. See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for for mat of OpenSWATH transition TSV file or SpectraST MRM file. (valid formats: 'tsv', 'mrm' , 'pqp', 'TraML') -in_type <type> Input file type -- default: determined from file extension or content (valid: 'tsv', 'mrm', 'pqp', 'TraML') -out <file>* Output file (valid formats: 'tsv', 'pqp', 'TraML') -out_type <type> Output file type -- default: determined from file extension or content Note: not all conversion paths work or make sense. (valid: 'tsv', 'pqp', 'TraML') 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) The following configuration subsections are valid: - algorithm Algorithm parameters section You can write an example INI file using the '-write_ini' option. Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor. For more information, please consult the online documentation for this tool: - http://www.openms.de/documentation/UTILS_TargetedFileConverter.html
INI file documentation of this tool: