OpenPepXL

Protein-protein cross-linking identification using labeled linkers.

Web Documentation for OpenPepXL

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: Overrides 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_light: Mass of the light cross-linker, linking two residues on one or two peptides
mass_iso_shift: Mass of the isotopic shift between the light and heavy linkers
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)
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

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

Output Ports

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

Popular Predecessors

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Views

OpenPepXL Std Output: The text sent to standard out during the execution of OpenPepXL.
OpenPepXL Error Output: The text sent to standard error during the execution of OpenPepXL. (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 the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.3

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, ZIB (GKN-Team) and the OpenMS Team

Plugin version: 3.2.0.202409181756

On NodePit since: 2024-10-17

Last update: 2024-11-21

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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