0 ×

NucleicAcidSearchEngine

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

Annotate nucleic acid identifications to MS/MS spectra.

Web Documentation for NucleicAcidSearchEngine

Options

version
Version of the tool that generated this parameters file.
decharge_ms2
Decharge the MS2 spectra for scoring
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 uncharged precursor mass)
mass_tolerance_unit
Unit of precursor mass tolerance
min_charge
Minimum precursor charge to be considered
max_charge
Maximum precursor charge to be considered
include_unknown_charge
Include MS2 spectra with unknown precursor charge - try to match them in any possible charge between 'min_charge' and 'max_charge', at the risk of a higher error rate
use_avg_mass
Use average instead of monoisotopic precursor masses (appropriate for low-resolution instruments)
use_adducts
Consider possible salt adducts (see 'precursor:potential_adducts') when matching precursor masses
potential_adducts
Adducts considered to explain mass differences. Format: 'Element:Charge(+/-)', i.e. the number of '+' or '-' indicates the charge, e.g. 'Ca:++' indicates +2. Only used if 'precursor:use_adducts' is set.
isotopes
Correct for mono-isotopic peak misassignments. E.g.: 1 = precursor may be misassigned to the first isotopic peak. Ignored if 'use_avg_mass' is set.
mass_tolerance
Fragment mass tolerance (+/- around fragment m/z)
mass_tolerance_unit
Unit of fragment mass tolerance
ions
Fragment ions to include in theoretical spectra
variable
Variable modifications
variable_max_per_oligo
Maximum number of residues carrying a variable modification per candidate oligonucleotide
resolve_ambiguities
Attempt to resolve ambiguous modifications (e.g. 'mA?' for 'mA'/'Am') based on a-B ions. This incurs a performance cost because two modifications have to be considered for each case. Requires a-B ions to be enabled in parameter 'fragment:ions'.
min_size
Minimum size an oligonucleotide must have after digestion to be considered in the search
max_size
Maximum size an oligonucleotide must have after digestion to be considered in the search, leave at 0 for no limit
missed_cleavages
Number of missed cleavages
enzyme
The enzyme used for RNA digestion
top_hits
Maximum number of top-scoring hits per spectrum that are reported ('0' for all hits)
decoy_pattern
String used as part of the accession to annotate decoy sequences (e.g. 'DECOY_'). Leave empty to skip the FDR/q-value calculation.
cutoff
Cut-off for FDR filtering; search hits with higher q-values will be removed
remove_decoys
Do not score hits to decoy sequences and remove them when filtering

Input Ports

Icon
Input file: spectra [mzML]
Icon
Input file: sequence database [fasta]

Output Ports

Icon
Output file: mzTab [mzTab]
Icon
Output file: idXML (for visualization in TOPPView) [idXML]
Icon
Output file: Targets for label-free quantification using FeatureFinderMetaboIdent ('id' input) [tsv]
Icon
Output file: theoretical MS2 spectra for precursor mass matches [mzML]
Icon
Output file: experimental MS2 spectra for precursor mass matches [mzML]

Views

NucleicAcidSearchEngine Std Output
The text sent to standard out during the execution of NucleicAcidSearchEngine.
NucleicAcidSearchEngine Error Output
The text sent to standard error during the execution of NucleicAcidSearchEngine. (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 4.3

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

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.

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.