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

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.)

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