0 ×

SiriusAdapter

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261314 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.
filter_by_num_masstraces
Features have to have at least x MassTraces. To use this parameter feature_only is neccessary
feature_only
Uses the feature information from in_featureinfo to reduce the search space to only MS2 associated with a feature
precursor_mz_tolerance
Tolerance window for precursor selection (Feature selection in regard to the precursor)
precursor_mz_tolerance_unit
Unit of the precursor_mz_tolerance
precursor_rt_tolerance
Tolerance window (left and right) for precursor selection [seconds]
isotope_pattern_iterations
Number of iterations that should be performed to extract the C13 isotope pattern. If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns.
no_masstrace_info_isotope_pattern
Use this flag if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used instead.
profile
Specify the used analysis profile
candidates
The number of candidates in the SIRIUS output.
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. 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 occurrence of these elements: CHNOP[5]S[8]Cl[1].
compound_timeout
Time out in seconds per compound. To disable the timeout set the value to 0
tree_timeout
Time out in seconds per fragmentation tree computation.
top_n_hits
The number of top hits for each compound written to the CSI:FingerID 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.
ion_tree
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.
most_intense_ms2
SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum)
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]
FeatureXML input with feature and adduct information [featurexml,opt.]

Output Ports

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

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

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform.