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CruxAdapter

Generic Workflow Nodes for KNIME: OpenMS version 2.6.0.202009301213 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Identifies MS/MS spectra using Crux.

Web Documentation for CruxAdapter

Options

version
Version of the tool that generated this parameters file.
extra_index_args
Extra arguments to be passed to tide-index
extra_search_args
Extra arguments to be passed to tide-search
extra_percolator_args
Extra arguments to be passed to percolator
precursor_mass_tolerance
Precursor monoisotopic mass tolerance (Crux parameter: peptide_mass_tolerance)
precursor_mass_units
Unit of precursor mass tolerance (amu, m/z or ppm)
fragment_bin_offset
In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da).
fragment_bin_width
Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended.
isotope_error
List of positive, non-zero integers.
run_percolator
Whether to run percolator after tide-search
enzyme
The enzyme used for peptide digestion.
digestion
Full, partial or non specific digestion
allowed_missed_cleavages
Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search
custom_enzyme
Specify rules for in silico digestion of protein sequences. Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site.
decoy_prefix
Specifies the prefix of the protein names that indicate a decoy
decoy_format
Decoy generation method either by reversing the sequence or shuffling it.
keep_terminal_aminos
Whether to keep N and C terminal in place or also shuffled / reversed.
cterm_modifications
Specifies C-terminal static and variable mass modifications on peptides. Specify a comma-separated list of C-terminal modification sequences of the form: X+21.9819 Default = <empty>.
nterm_modifications
Specifies N-terminal static and variable mass modifications on peptides. Specify a comma-separated list of N-terminal modification sequences of the form: 1E-18.0106,C-17.0265 Default = <empty>.
modifications
Expression for static and variable mass modifications to include. Specify a comma-separated list of modification sequences of the form: C+57.02146,2M+15.9949,1STY+79.966331,... Default = C+57.02146.
test_fdr
False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results.
train_fdr
False discovery rate threshold to define positive examples in training.
deisotope
Deisotope spectra before searching
report_decoys
Include decoys in the final reported dataset
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
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)

Input Ports

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Input file [mzML]
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FASTA file [FASTA]

Output Ports

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Output file [idXML]

Views

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

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Installation

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

KNIME 4.2

A zipped version of the software site can be downloaded here.

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Developers

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