PeptideDataBaseSearchFI

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)

enzyme

The enzyme used for peptide digestion.

decoys

Should decoys be generated?

mass_tolerance

+/- tolerance for 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.

isotopes

Corrects for mono-isotopic peak misassignments. (E.g.: 1 = prec. may be misassigned to first isotopic peak)

isotope_error_min

Minimum allowed precursor isotope error

isotope_error_max

Maximum allowed precursor isotope error

open_window_lower

lower bound of the open precursor window

open_window_upper

upper bound of the open precursor window

mass_tolerance

Fragment mass tolerance

mass_tolerance_unit

Unit of fragment m

min_mz

Minimal fragment mz for database

max_mz

Maximal fragment mz for database

min_matched_ions

Minimal number of matched ions to report a PSM

max_charge

max fragment charge

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

PSM

Annotations added to each PSM.

min_size

Minimum size a peptide must have after digestion to be considered in the search.

max_size

Maximum size a peptide must have after digestion to be considered in the search (0 = disabled).

missed_cleavages

Number of missed cleavages.

motif

If set, only peptides that contain this motif (provided as RegEx) will be considered.

min_mass

Minimal peptide mass for database

max_mass

Maximal peptide mass for database

top_hits

Maximum number of top scoring hits per spectrum that are reported.

max_candidates_per_spectrum

The number of initial hits for which we calculate a score

add_y_ions

Add peaks of y-ions to the spectrum

add_b_ions

Add peaks of b-ions to the spectrum

add_a_ions

Add peaks of a-ions to the spectrum

add_c_ions

Add peaks of c-ions to the spectrum

add_x_ions

Add peaks of x-ions to the spectrum

add_z_ions

Add peaks of z-ions to the spectrum

Views

PeptideDataBaseSearchFI Std Output

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

PeptideDataBaseSearchFI Error Output

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