OpenPepXLLF

Options

version

Version of the tool that generated this parameters file.

decoy_string

String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins.

decoy_prefix

Set to true, if the decoy_string is a prefix of accessions in the protein database. Otherwise it is a suffix.

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

Width of precursor mass tolerance window

mass_tolerance_unit

Unit of precursor mass tolerance.

min_charge

Minimum precursor charge to be considered.

max_charge

Maximum precursor charge to be considered.

corrections

Monoisotopic peak correction. Matches candidates for possible monoisotopic precursor peaks for experimental mass m and given numbers n at masses (m - n * (C13-C12)). These should be ordered from more extreme to less extreme corrections. Numbers later in the list will be preferred in case of ambiguities.

mass_tolerance

Fragment mass tolerance

mass_tolerance_xlinks

Fragment mass tolerance for cross-link ions

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.

missed_cleavages

Number of missed cleavages.

enzyme

The enzyme used for peptide digestion.

residue1

Comma separated residues, that the first side of a bifunctional cross-linker can attach to

residue2

Comma separated residues, that the second side of a bifunctional cross-linker can attach to

mass

Mass of the light cross-linker, linking two residues on one or two peptides

mass_mono_link

Possible masses of the linker, when attached to only one peptide

name

Name of the searched cross-link, used to resolve ambiguity of equal masses (e.g. DSS or BS3)

number_top_hits

Number of top hits reported for each spectrum pair

deisotope

Set to true, if the input spectra should be deisotoped before any other processing steps. If set to auto the spectra will be deisotoped, if the fragment mass tolerance is < 0.1 Da or < 100 ppm (0.1 Da at a mass of 1000)

use_sequence_tags

Use sequence tags (de novo sequencing of short fragments) to filter out candidates before scoring. This will make the search faster, but can impact the sensitivity positively or negatively, depending on the dataset.

sequence_tag_min_length

Minimal length of sequence tags to use for filtering candidates. Longer tags will make the search faster but much less sensitive. Ignored if 'algorithm:use_sequence_tags' is false.

b_ions

Search for peaks of b-ions.

y_ions

Search for peaks of y-ions.

a_ions

Search for peaks of a-ions.

x_ions

Search for peaks of x-ions.

c_ions

Search for peaks of c-ions.

z_ions

Search for peaks of z-ions.

neutral_losses

Search for neutral losses of H2O and H3N.

Views

OpenPepXLLF Std Output

The text sent to standard out during the execution of OpenPepXLLF.

OpenPepXLLF Error Output

The text sent to standard error during the execution of OpenPepXLLF. (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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