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SiriusAdapter

Generic Workflow Nodes for KNIME: OpenMS version 2.3.0.201712211252 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Tool for metabolite identification using single and tandem mass spectrometry

Web Documentation for SiriusAdapter

Options

version
Version of the tool that generated this parameters file.
profile
Specify the used analysis profile
candidates
The number of candidates in the output. Default 5 best candidates
database
search formulas in given database
noise
median intensity of noise peaks
ppm_max
allowed ppm for decomposing masses
isotope
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.
elements
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.
number
The number of compounds used in the output
auto_charge
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.
iontree
Print molecular formulas and node labels with the ion formula instead of the neutral formula
no_recalibration
If this option is set, SIRIUS will not recalibrate the spectrum during the analysis.
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overwrite tool specific checks.
test
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]

Views

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Update Site

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