Export MS/MS data in .MGF format for GNPS (http://gnps.ucsd.edu).

GNPS (Global Natural Products Social Molecular Networking, http://gnps.ucsd.edu) is an open-access knowledge base for community-wide organisation and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. The GNPS web-platform makes possible to perform spectral library search against public MS/MS spectral libraries, as well as to perform various data analysis such as MS/MS molecular networking, network annotation propagation (http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006089), and the Dereplicator-based annotation (https://www.nature.com/articles/nchembio.2219). The GNPS manuscript is available here: https://www.nature.com/articles/nbt.3597

This tool was developed for the OpenMS-GNPS workflow. It can be accessed on GNPS (https://gnps.ucsd.edu/ProteoSAFe/static/gnps-experimental.jsp). The steps used by that workflow are as following: 1. Input mzML files 2. Run the FeatureFinderMetabo tool 3. Run the IDMapper tool 4. Run the MapAlignerPoseClustering tool 5. Run the FeautureLinkerUnlabeledKD tool 6. Run the FileConverter tool (output FeatureXML format) 7. Run the MetaboliteAdductDecharger 8. Run the GNPSExport to export an .MGF 9. Upload the .MGF file on http://gnps.ucsd.edu and follow the instructions here: https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/

The command line parameters of this tool are:

GNPSExport -- Tool to export consensus features into MGF format
Full documentation: 
Version: 2.5.0-nightly-2020-03-06 Mar  7 2020, 01:22:16, Revision: 84b1398
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:
  GNPSExport <options>

Options (mandatory options marked with '*'):
  -in_cm <file>*                        Input file containing consensus elements with 'peptide' annotations 
                                        (valid formats: 'consensusXML')
  -in_mzml <files>*                     Original mzml files containing ms/ms spectrum information (valid form
                                        ats: 'mzML')
  -out <file>*                          Output MGF file (valid formats: 'mgf')
  -output_type <choice>                 Specificity of mgf output information (default: 'full_spectra' valid:
                                        'full_spectra', 'merged_spectra')
  -precursor_mz_tolerance <num>         Tolerance mz window for precursor selection (default: '1.0e-04')
  -precursor_rt_tolerance <num>         Tolerance rt window for precursor selection (default: '5.0')

Options for exporting mgf file with merged spectra per feature:
  -merged_spectra:cos_similarity <num>  Cosine similarity threshold for merged_spectra output (default: '0.95
                                        ')

                                        
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 (defau
                                        lt: '1')
  -write_ini <file>                     Writes the default configuration file
  --help                                Shows options
  --helphelp                            Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+GNPSExportTool to export consensus features into MGF format

version2.5.0-nightly-2020-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'GNPSExport'

in_cm input file containing consensus elements with 'peptide' annotationsinput file*.consensusXML

in_mzml[] original mzml files containing ms/ms spectrum informationinput file*.mzML

out Output MGF fileoutput file*.mgf

output_typefull_spectra specificity of mgf output informationfull_spectra,merged_spectra

precursor_mz_tolerance1.0e-04 Tolerance mz window for precursor selection

precursor_rt_tolerance5.0 Tolerance rt window for precursor selection

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

+++merged_spectraOptions for exporting mgf file with merged spectra per feature

cos_similarity0.95 Cosine similarity threshold for merged_spectra output