OpenNuXL

Annotate RNA/DNA-peptide cross-links in MS/MS spectra.

Web Documentation for OpenNuXL

Options

version: Version of the tool that generated this parameters file.
output_folder: Store intermediate files (and final result) also in this output folder. Convenient for TOPPAS/KNIME/etc. users because these files are otherwise only stored in tmp folders.
filter: Filtering steps applied to results.
window_size: Peak window for spectra precprocessing.
peak_count: Retained peaks in peak window.
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: Precursor mass tolerance (+/- around precursor m/z).
mass_tolerance_unit: Unit of precursor mass tolerance.
min_charge: Minimum precursor charge to be considered.
max_charge: Maximum precursor charge to be considered.
isotopes: Corrects for mono-isotopic peak misassignments. (E.g.: 1 = prec. may be misassigned to first isotopic peak).
mass_tolerance: Fragment mass tolerance (+/- around fragment m/z).
mass_tolerance_unit: Unit of fragment mass tolerance.
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.
max_size: Maximum size a peptide may have after digestion to be considered in the search.
missed_cleavages: Number of missed cleavages.
enzyme: The enzyme used for peptide digestion.
top_hits: Maximum number of top scoring hits per spectrum that are reported.
peptideFDR: Maximum q-value of non-cross-linked peptides. (0 = disabled).
xlFDR: Maximum q-value of cross-linked peptides at the PSM-level. (0 or 1 = disabled). If multiple values are provided, multiple output files will be created.
xl_peptidelevel_FDR: Maximum q-value of cross-linked peptides at the peptide-level. (0 or 1 = disabled). Needs to have same size as PSM-level FDR. Filtering is applied together with the correpsonding value in the report:xlFDR list.
presets: Set precursor and fragment adducts from presets (recommended). Custom presets can be defined in a 'nuxl_presets.json' file placed in the share/OpenMS/NUXL/ directory or specified via NuXL:presets_file.
length: Oligonucleotide maximum length. 0 = disable search for NA variants.
sequence: Sequence to restrict the generation of oligonucleotide chains. (disabled for empty sequence).
target_nucleotides: format: target nucleotide=empirical formula of nucleoside monophosphate e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU or e.g. Y=C10H14N5O7PS where Y represents tG.
nt_groups: Restrict which nucleotides can cooccur in a precursor adduct to be able to search both RNA and DNA (format: 'AU CG').
mapping: format: source->target e.g. A->A, ..., U->U, U->X.
can_cross_link: format: 'U' if only U forms cross-links. 'CATG' if C, A, G, and T form cross-links.
fragment_adducts: format: [target nucleotide]:[formula] or [precursor adduct]->[fragment adduct formula];[name]: e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O->C9H11N2O8P1;U-H2O'.
modifications: format: empirical formula e.g U: U:-H2O, ..., U:H2O+PO3.
scoring: Scoring algorithm used in prescoring (fast: total-loss only, slow: all losses).
decoys: Generate decoys internally (recommended).
decoy_factor: Ratio of decoys to targets.
CysteineAdduct: Use this flag if the +152 adduct is expected.
filter_fractional_mass: Use this flag to filter non-crosslinks by fractional mass.
carbon_labeled_fragments: Generate fragment shifts assuming full labeling of carbon (e.g. completely labeled U13).
only_xl: Only search cross-links and ignore non-cross-linked peptides.
filter_small_peptide_mass: Filter precursor that can only correspond to non-crosslinks by mass.
marker_ions_tolerance: Tolerance used to determine marker ions (Da).
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts
target_nucleotides
mapping
can_cross_link
modifications
fragment_adducts

Input Ports

: input file [mzML,raw]
: The .NET framework executable. Only required on linux and mac. [,opt.]
: The ThermoRawFileParser executable. [,opt.]
: The protein database used for identification. [fasta]
: Percolator executable of the installation e.g. 'percolator.exe' [,opt.]
: Optional custom path to nuxl_presets.json file. If not provided, the default file in share/OpenMS/NUXL/ will be used. [json,opt.]

Output Ports

: output file [idXML]
: tsv output file [tsv]
: XL output file with group q-values calculated at the XL PSM-level. Generated for the highest FDR threshold in report:xlFDR. [idXML]

Popular Predecessors

No recommendations found

Popular Successors

No recommendations found

Views

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

Workflows

No workflows found

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.

Installation

To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.9

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

Plugin version: 3.5.0.202512111229

On NodePit since: 2025-12-12

Last update: 2025-12-13

KNIME versions: Since v5.9

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!