TargetedFileConverter

Converts different transition files for targeted proteomics and metabolomics analysis.

Can convert multiple formats to and from TraML (standardized transition format). It supports the OpenSWATH TSV format as well as the PQP format for transitions.

The OpenSWATH transition TSV files need to have the following headers, all fields need to be separated by tabs:

• PrecursorMz (float)
• ProductMz (float)
• Tr_recalibrated (float) (normalized retention time)
• transition_name (free text, needs to be unique for each transition [in this file])
• CollisionEnergy (float)
• LibraryIntensity (float)
• transition_group_id (free text, designates the transition group [e.g. peptide] to which this transition belongs)
• decoy (1==decoy, 0== no decoy; determines whether the transition is a decoy transition or not)
• PeptideSequence (free text, sequence only (no modifications) )
• ProteinName (free text)
• Annotation (free text, e.g. y7)
• FullUniModPeptideName (free text, should contain modifications¹)
• PrecursorCharge (integer, contains the charge of the precursor)
• PeptideGroupLabel (free text, designates to which peptide label group (as defined in MS:1000893) the peptide belongs to²)
• LabelType (free text, optional description of which label was used, e.g. heavy or light)
• UniprotID (free text)
• FragmentType (free text, contains the type of the fragment, e.g. "b" or "y")
• FragmentCharge (integer, contains the fragment charge)
• FragmentSeriesNumber (integer, e.g. for y7 use "7" here)

Remarks:

• 1. modifications should be supplied inside the sequence using UniMod identifiers or freetext identifiers that are understood by OpenMS.
  example: PEPT(Phosphorylation)IDE(UniMod:27)A )
• 2. peptide label groups designate groups of peptides that are isotopically modified forms of the same peptide species. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
  example:
  PEPTIDEAK -> gets label "PEPTIDEAK_gr1"
  PEPTIDEAK[+8] -> gets label "PEPTIDEAK_gr1"
  PEPT(Phosphorylation)IDEAK -> gets label "PEPTIDEAK_gr2"
  PEPT(Phosphorylation)IDEAK[+8] -> gets label "PEPTIDEAK_gr2"
  

The command line parameters of this tool are:

TargetedFileConverter -- Converts different transition files for targeted proteomics / metabolomics analysis.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

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: that 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.
Have a look at the OpenMS documentation for more information.

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+TargetedFileConverterConverts different transition files for targeted proteomics / metabolomics analysis.

version2.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'TargetedFileConverter'

in Input file to convert.
See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file.input file*.tsv,*.mrm,*.pqp,*.TraML

in_type input file type -- default: determined from file extension or content
tsv,mrm,pqp,TraML

out Output fileoutput file*.tsv,*.pqp,*.TraML

out_type Output file type -- default: determined from file extension or content
Note: that not all conversion paths work or make sense.tsv,pqp,TraML

legacy_traml_idfalse PQP to TraML: Should legacy TraML IDs be used?true,false

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

+++algorithmAlgorithm parameters section

retentionTimeInterpretationiRT How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)iRT,seconds,minutes

override_group_label_checkfalse Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group). Only turn this off if you know what you are doing.true,false

force_invalid_modsfalse Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)true,false