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RNPxlSearch

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

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

Web Documentation for RNPxlSearch

Options

version
Version of the tool that generated this parameters file.
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 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.
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.
length
Oligonucleotide maximum length. 0 = disable search for RNA 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 (Formate e.g.: 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 -H2O, ..., H2O+PO3
scoring
Scoring algorithm used in prescoring (fast: total-loss, slow: all losses).
decoys
Generate decoy sequences and spectra.
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).

Input Ports

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input file [mzML]
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input file [fasta]

Output Ports

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output file [idXML]
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tsv output file [tsv]

Views

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