IconSiriusAdapter0 ×

Generic Workflow Nodes for KNIME: OpenMS version by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Tool for metabolite identification using single and tandem mass spectrometry

Web Documentation for SiriusAdapter


Version of the tool that generated this parameters file.
Specify the used analysis profile
The number of candidates in the output. Default 5 best candidates
search formulas in given database
median intensity of noise peaks
allowed ppm for decomposing masses
how to handle isotope pattern data. Use 'score' to use them for ranking or 'filter' if you just want to remove candidates with bad isotope pattern. With 'both' you can use isotopes for filtering and scoring (default). Use 'omit' to ignore isotope pattern.
The allowed elements. Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the maximal allowed occurence of these elements: CHNOP[5]S[8]Cl[1]. By default CHNOP[5]S is used.
The number of compounds used in the output
Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default. With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak.
Print molecular formulas and node labels with the ion formula instead of the neutral formula
If this option is set, SIRIUS will not recalibrate the spectrum during the analysis.
Name of log file (created only when specified)
Sets the debug level
Sets the number of threads allowed to be used by the TOPP tool
Disables progress logging to command line
Overwrite tool specific checks.
Enables the test mode (needed for internal use only)

Input Ports

MzML Input file [mzml]

Output Ports

MzTab Output file for SiriusAdapter results [tsv]
MzTab ouput file for CSI:FingerID, if this parameter is given, SIRIUS will search for a molecular structure using CSI:FingerID after determining the sum formula [tsv,Inactive]


SiriusAdapter Std Output
The text sent to standard out during the execution of SiriusAdapter.
SiriusAdapter Error Output
The text sent to standard error during the execution of SiriusAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: OpenMS from the following update site:

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