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AssayGeneratorMetabo (version 2.8+galaxy0)

The Sirius executable:

Provide a full or relative path, or make sure it can be found in your PATH environment select txt data sets(s)

Run tool in batch mode for -in:

MzML input file(s) used for assay library generation:

select mzml data sets(s)

Run tool in batch mode for -in_id:

FeatureXML input file(s) containing identification information:

(e.g. AccurateMassSearch) select featurexml data sets(s)

File type of output out (Assay library output file):

Fragment annotation method:

Mz tolerance for the resolution of identification ambiguity over multiple files:

RT tolerance in seconds for the resolution of identification ambiguity over multiple files:

Filter compound based on total occurrence in analysed samples:

Filters annotations based on the explained intensity of the peaks in a spectrum:

Decoys will be generated using the fragmentation tree re-rooting approach:

This option does only work in combination with the fragment annotation via Sirius

Uses different methods for decoy generation:

Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping fragments of the highest intensity fragments chosen, by adding -CH2 mass to the overlapping fragments. 'Add_shift' will add a -CH2 mass shift to the target fragments and use them as additional decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, add_shift)

Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used):

Use exact mass for precursor and fragment annotations:

Excludes precursor in ms2 from transition list:

Max m/z distance of the precursor entries of two spectra to be merged in [Da]:

Tolerance window (left and right) for precursor selection [seconds], for consensus spectrum generation (only available without fragment annotation):

Use features without identification information:

Minimal number of transitions:

Maximal number of transitions:

Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation:

Further transitions need at least x% of the maximum intensity (default 5%):

deisotopings

deisotoping 0

Advanced Options

Advanced Options 0

Optional outputs: