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).

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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