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OpenPepXLLF

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

Tool for protein-protein cross linking with label-free linkers.

Web Documentation for OpenPepXLLF

Options

version
Version of the tool that generated this parameters file.
decoy_string
String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins.
decoy_prefix
Set to true, if the decoy_string is a prefix of accessions in the protein database. Otherwise it is a suffix.
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)
mass_tolerance
Width of precursor mass tolerance window
mass_tolerance_unit
Unit of precursor mass tolerance.
min_charge
Minimum precursor charge to be considered.
max_charge
Maximum precursor charge to be considered.
corrections
Monoisotopic peak correction. Matches candidates for possible monoisotopic precursor peaks for experimental mass m and given numbers n at masses (m - n * (C13-C12)). These should be ordered from more extreme to less extreme corrections. Numbers later in the list will be preferred in case of ambiguities.
mass_tolerance
Fragment mass tolerance
mass_tolerance_xlinks
Fragment mass tolerance for cross-link ions
mass_tolerance_unit
Unit of fragment m
fixed
Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'
variable
Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Oxidation (M)'
variable_max_per_peptide
Maximum number of residues carrying a variable modification per candidate peptide
min_size
Minimum size a peptide must have after digestion to be considered in the search.
missed_cleavages
Number of missed cleavages.
enzyme
The enzyme used for peptide digestion.
residue1
Comma separated residues, that the first side of a bifunctional cross-linker can attach to
residue2
Comma separated residues, that the second side of a bifunctional cross-linker can attach to
mass
Mass of the light cross-linker, linking two residues on one or two peptides
mass_mono_link
Possible masses of the linker, when attached to only one peptide
name
Name of the searched cross-link, used to resolve ambiguity of equal masses (e.g. DSS or BS3)
number_top_hits
Number of top hits reported for each spectrum pair
deisotope
Set to true, if the input spectra should be deisotoped before any other processing steps. If set to auto the spectra will be deisotoped, if the fragment mass tolerance is < 0.1 Da or < 100 ppm (0.1 Da at a mass of 1000)
use_sequence_tags
Use sequence tags (de novo sequencing of short fragments) to filter out candidates before scoring. This will make the search faster, but can impact the sensitivity positively or negatively, depending on the dataset.
sequence_tag_min_length
Minimal length of sequence tags to use for filtering candidates. Longer tags will make the search faster but much less sensitive. Ignored if 'algorithm:use_sequence_tags' is false.
b_ions
Search for peaks of b-ions.
y_ions
Search for peaks of y-ions.
a_ions
Search for peaks of a-ions.
x_ions
Search for peaks of x-ions.
c_ions
Search for peaks of c-ions.
z_ions
Search for peaks of z-ions.
neutral_losses
Search for neutral losses of H2O and H3N.

Input Ports

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Input file containing the spectra. [mzML]
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Input file containing the protein database. [fasta]
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Input file containing the decoy protein database. Decoys can also be included in the normal database file instead (or additionally). [fasta,opt.]

Output Ports

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Results in idXML format (at least one of these output parameters should be set, otherwise you will not have any results). [idXML]
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Results in mzIdentML (.mzid) format (at least one of these output parameters should be set, otherwise you will not have any results) [mzid]
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Results in the xquest.xml format (at least one of these output parameters should be set, otherwise you will not have any results). [xquest.xml]
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Matched spectra in the xQuest .spec.xml format for spectra visualization in the xQuest results manager. [spec.xml]

Views

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