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LuciphorAdapter

Generic Workflow Nodes for KNIME: OpenMS version 2.5.0.202002201806 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Modification site localisation using LuciPHOr2.

Web Documentation for LuciphorAdapter

Options

version
Version of the tool that generated this parameters file.
fragment_method
Fragmentation method
fragment_mass_tolerance
Tolerance of the peaks in the fragment spectrum
fragment_error_units
Unit of fragment mass tolerance
min_mz
Do not consider peaks below this value for matching fragment ions
target_modifications
List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'
neutral_losses
List the types of neutral losses that you want to consider. The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = <RESDIUES> -<NEUTRAL_LOSS_MOLECULAR_FORMULA> <MASS_LOST>
decoy_mass
How much to add to an amino acid to make it a decoy
decoy_neutral_losses
For handling the neutral loss from a decoy sequence. The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -<NEUTRAL_LOSS_MOLECULAR_FORMULA> <MASS_LOST>
max_charge_state
Do not consider PSMs with a charge state above this value
max_peptide_length
Restrict scoring to peptides with a length shorter than this value
max_num_perm
Maximum number of permutations a sequence can have
modeling_score_threshold
Minimum score a PSM needs to be considered for modeling
scoring_threshold
PSMs below this value will be discarded
min_num_psms_model
The minimum number of PSMs you need for any charge state in order to build a model for it
num_threads
For multi-threading, 0 = use all CPU found by JAVA
run_mode
Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported
rt_tolerance
Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)
java_memory
Maximum Java heap size (in MB)
java_permgen
Maximum Java permanent generation space (in MB); only for Java 7 and below
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

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Input spectrum file [mzML]
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Protein/peptide identifications file [idXML]
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The Java executable. Usually Java is on the system PATH. If Java is not found, use this parameter to specify the full path to Java [,opt.]

Output Ports

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Output file [idXML]

Views

LuciphorAdapter Std Output
The text sent to standard out during the execution of LuciphorAdapter.
LuciphorAdapter Error Output
The text sent to standard error during the execution of LuciphorAdapter. (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)

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.2
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Developers

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