OpenMS
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Generates an assay library using DDA data (Metabolomics)
potential predecessor tools | → AssayGeneratorMetabo → | potential successor tools |
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FeatureFinderMetabo | OpenSWATH pipeline | |
AccurateMassSearch |
Build an assay library from DDA data (MS and MS/MS) (mzML). Please provide a list of features found in the data (featureXML).
Features can be detected using the FeatureFinderMetabo (FFM) and identifcation information can be added using the AccurateMassSearch featureXML output.
If the FeatureFinderMetabo featureXML does not contain any identifications the "use_known_unknowns" flag is used automatically.
Internal procedure AssayGeneratorMetabo:
The command line parameters of this tool are:
AssayGeneratorMetabo -- Assay library generation from DDA data (Metabolomics) Full documentation: http://www.openms.de/doxygen/release/3.3.0/html/TOPP_AssayGeneratorMetabo.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: AssayGeneratorMetabo <options> Options (mandatory options marked with '*'): -in <file(s)>* MzML input file(s) used for assay library generation (val id formats: 'mzML') -in_featureinfo <file(s)>* FeatureXML input file(s) containing identification inform ation (e.g. AccurateMassSearch) (valid formats: 'featureX ML') -out <file>* Assay library output file (valid formats: 'tsv', 'traML', 'pqp') -ambiguity_resolution_mz_tolerance <num> Mz tolerance for the resolution of identification ambigui ty over multiple files (default: '10.0') -ambiguity_resolution_rt_tolerance <num> RT tolerance in seconds for the resolution of identificat ion ambiguity over multiple files (default: '10.0') -total_occurrence_filter <num> Filter compound based on total occurrence in analysed samples (default: '0.1') (min: '0.0' max: '1.0') -method <choice> Spectrum with the highest precursor intensity or a consen sus spectrum is used for assay library construction (if no fragment annotation is used). (default: 'highest_inten sity') (valid: 'highest_intensity', 'consensus_spectrum') -exclude_ms2_precursor Excludes precursor in ms2 from transition list -use_known_unknowns Use features without identification information -min_transitions <int> Minimal number of transitions (default: '3') -max_transitions <int> Maximal number of transitions (default: '6') -cosine_similarity_threshold <num> Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation (defau lt: '0.98') -transition_threshold <num> Further transitions need at least x% of the maximum inten sity (default 5%) (default: '5.0') -precursor_mz_distance <num> Max m/z distance of the precursor entries of two spectra to be merged in [Da]. (default: '1.0e-04') -precursor_consensus_spectrum_rt_tolerance <num> Tolerance window (left and right) for precursor selection [seconds], for consensus spectrum generation (only avail able without fragment annotation) (default: '5.0') -deisotoping_use_deisotoper Use Deisotoper (if no fragment annotation is used) -deisotoping_fragment_tolerance <num> Tolerance used to match isotopic peaks (default: '1.0') -deisotoping_fragment_unit <choice> Unit of the fragment tolerance (default: 'ppm') (valid: 'ppm', 'Da') -deisotoping_min_charge <num> The minimum charge considered (default: '1') (min: '1') -deisotoping_max_charge <num> The maximum charge considered (default: '1') (min: '1') -deisotoping_min_isopeaks <num> The minimum number of isotopic peaks (at least 2) require d for an isotopic cluster (default: '2') (min: '2') -deisotoping_max_isopeaks <num> The maximum number of isotopic peaks (at least 2) conside red for an isotopic cluster (default: '3') (min: '3') -deisotoping_keep_only_deisotoped Only monoisotopic peaks of fragments with isotopic patter n are retained -deisotoping_annotate_charge Annotate the charge to the peaks -filter_by_num_masstraces <number> Number of mass traces each feature has to have to be incl uded. To use this parameter, setting the feature_only flag is necessary (default: '1') (min: '1') -precursor_mz_tolerance <value> Tolerance window for precursor selection (Feature selecti on in regard to the precursor) (default: '10.0') -precursor_mz_tolerance_unit <choice> Unit of the preprocessing_precursor_mz_tolerance (default : 'ppm') (valid: 'ppm', 'Da') -precursor_rt_tolerance <value> Tolerance window (left and right) for precursor selection [seconds] (default: '5.0') -feature_only <choice> Uses the feature information from in_featureinfo to reduc e the search space to MS2 associated with a feature (defa ult: 'false') (valid: 'false', 'true') 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: