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CometAdapter

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

Annotates MS/MS spectra using Comet.

Web Documentation for CometAdapter

Options

version
Version of the tool that generated this parameters file.
precursor_mass_tolerance
Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance). See also precursor_error_units to set the unit.
precursor_error_units
Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)
isotope_error
This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement. Use -8/-4/0/4/8 only for SILAC.
fragment_mass_tolerance
This is half the bin size, which is used to segment the MS/MS spectrum. Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size.
fragment_error_units
Fragment monoisotopic mass error units
fragment_bin_offset
Offset of fragment bins. Recommended by Comet: low-res: 0.4, high-res: 0.0
instrument
Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only
use_A_ions
use A ions for PSM
use_B_ions
use B ions for PSM
use_C_ions
use C ions for PSM
use_X_ions
use X ions for PSM
use_Y_ions
use Y ions for PSM
use_Z_ions
use Z ions for PSM
use_NL_ions
use neutral loss (NH3, H2O) ions from b/y for PSM
enzyme
The enzyme used for peptide digestion.
second_enzyme
Additional enzyme used for peptide digestion.
num_enzyme_termini
Specify the termini where the cleavage rule has to match
missed_cleavages
Number of possible cleavage sites missed by the enzyme. It has no effect if enzyme is unspecific cleavage.
min_peptide_length
Minimum peptide length to consider.
max_peptide_length
Maximum peptide length to consider.
num_hits
Number of peptide hits in output file
precursor_charge
Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3
override_charge
_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state. For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range
ms_level
MS level to analyze, valid are levels 2 (default) or 3
activation_method
If not ALL, only searches spectra of the given method
digest_mass_range
MH+ peptide mass range to analyze
max_fragment_charge
Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1. (Allowed max 5)
max_precursor_charge
set maximum precursor charge state to analyze (allowed max 9)
clip_nterm_methionine
If set to true, also considers the peptide sequence w/o N-term methionine separately and applies appropriate N-term mods to it
spectrum_batch_size
max. number of spectra to search at a time; use 0 to search the entire scan range in one batch
mass_offsets
One or more mass offsets to search (values subtracted from deconvoluted precursor mass). Has to include 0.0 if you want the default mass to be searched.
minimum_peaks
Required minimum number of peaks in spectrum to search (default 10)
minimum_intensity
Minimum intensity value to read in
remove_precursor_peak
no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD). phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance
remove_precursor_tolerance
one-sided tolerance for precursor removal in Thompson
clear_mz_range
for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0
fixed_modifications
Fixed modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
variable_modifications
Variable modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
binary_modifications
List of modification group indices. Indices correspond to the binary modification index used by comet to group individually searched lists of variable modifications. Note: if set, both variable_modifications and binary_modifications need to have the same number of entries as the N-th entry corresponds to the N-th variable_modification. if left empty (default), all entries are internally set to 0 generating all permutations of modified and unmodified residues. For a detailed explanation please see the parameter description in the Comet help.
max_variable_mods_in_peptide
Set a maximum number of variable modifications per peptide
require_variable_mod
If true, requires at least one variable modification per peptide
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]
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Default Comet params file. All parameters of this take precedence. A template file can be generated using 'comet.exe -p' [txt,opt.]

Output Ports

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Output file [idXML]
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Output file - for Percolator input [tsv]

Views

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

Workflows

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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