TargetedFileConverter

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:

• TraML
• OpenSWATH TSV transition lists
• OpenSWATH PQP SQLite files
• SpectraST MRM transition lists
• Skyline transition lists
• Spectronaut transition lists

Transition lists can be either comma- or tab-separated. Modifications should be provided in UniMod format¹, but can also be provided in TPP format. The following columns are required:

• PrecursorMz* (float)
• ProductMz* (float; synonyms: FragmentMz)
• LibraryIntensity* (float; synonyms: RelativeFragmentIntensity)
• NormalizedRetentionTime* (float; synonyms: RetentionTime, Tr_recalibrated, iRT, RetentionTimeCalculatorScore) (normalized retention time)

For targeted proteomics files, the following additional columns should be provided:

• ProteinId** (free text; synonyms: ProteinName)
• PeptideSequence** (free text, sequence only (no modifications); synonyms: Sequence, StrippedSequence)
• ModifiedPeptideSequence** (free text, should contain modifications¹; synonyms: FullUniModPeptideName, FullPeptideName, ModifiedSequence)
• PrecursorCharge** (integer, contains the charge of the precursorl synonyms: Charge)
• ProductCharge** (integer, contains the fragment charge; synonyms: FragmentCharge)
• FragmentType (free text, contains the type of the fragment, e.g. "b" or "y")
• FragmentSeriesNumber (integer, e.g. for y7 use "7" here; synonyms: FragmentNumber)

OpenSWATH uses grouped transitions to detect candidate analyte signals. These groups are by default generated based on the input, but can also be manually specified:

• TransitionGroupId (free text, designates the transition group [e.g. peptide] to which this transition belongs; synomys: TransitionGroupName, transition_group_id)
• TransitionId (free text, needs to be unique for each transition [in this file]; synonyms: TransitionName, transition_name)
• Decoy (1: decoy, 0: target, i.e. no decoy; determines whether the transition is a decoy transition or not, synomys: decoy, isDecoy)
• PeptideGroupLabel (free text, designates to which peptide label group (as defined in MS:1000893) the peptide belongs to²)
• DetectingTransition (1: use transition to detect peak group, 0: don't use transition for detection; synonyms: detecting_transition)
• IdentifyingTransition (1: use transition for peptidoform inference using IPF, 0: don't use transition for identification; synonyms: identifying_transition)
• QuantifyingTransition (1: use transition to quantify peak group, 0: don't use transition for quantification; synonyms: quantifying_transition)

Optionally, the following columns can be specified but they are not actively used by OpenSWATH:

• CollisionEnergy (float; synonyms: CE)
• Annotation (free text, e.g. y7)
• UniprotId (free text; synonyms: UniprotID)
• LabelType (free text, optional description of which label was used, e.g. heavy or light)

For targeted metabolomics files, the following fields are also supported:

• CompoundName** (synonyms: CompoundId)
• SMILES
• SumFormula

Fields indicated with * are strictly required while fields indicated with ** are only required in the specific context (proteomics or metabolomics).

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 Apr 18 2018, 18:59:40, Revision: 2cda6bd
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: 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