CruxAdapter

Options

version

Version of the tool that generated this parameters file.

extra_index_args

Extra arguments to be passed to tide-index

extra_search_args

Extra arguments to be passed to tide-search

extra_percolator_args

Extra arguments to be passed to percolator

precursor_mass_tolerance

Precursor monoisotopic mass tolerance (Crux parameter: peptide_mass_tolerance)

precursor_mass_units

Unit of precursor mass tolerance (amu, m/z or ppm)

fragment_bin_offset

In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da).

fragment_bin_width

Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended.

isotope_error

List of positive, non-zero integers.

run_percolator

Whether to run percolator after tide-search

enzyme

The enzyme used for peptide digestion.

digestion

Full, partial or non specific digestion

allowed_missed_cleavages

Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search

custom_enzyme

Specify rules for in silico digestion of protein sequences. Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site.

decoy_prefix

Specifies the prefix of the protein names that indicate a decoy

decoy_format

Decoy generation method either by reversing the sequence or shuffling it.

keep_terminal_aminos

Whether to keep N and C terminal in place or also shuffled / reversed.

cterm_modifications

Specifies C-terminal static and variable mass modifications on peptides. Specify a comma-separated list of C-terminal modification sequences of the form: X+21.9819 Default = <empty>.

nterm_modifications

Specifies N-terminal static and variable mass modifications on peptides. Specify a comma-separated list of N-terminal modification sequences of the form: 1E-18.0106,C-17.0265 Default = <empty>.

modifications

Expression for static and variable mass modifications to include. Specify a comma-separated list of modification sequences of the form: C+57.02146,2M+15.9949,1STY+79.966331,... Default = C+57.02146.

test_fdr

False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results.

train_fdr

False discovery rate threshold to define positive examples in training.

deisotope

Deisotope spectra before searching

report_decoys

Include decoys in the final reported dataset

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)

Views

CruxAdapter Std Output

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

CruxAdapter Error Output

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