IDFileConverter

Options

version

Version of the tool that generated this parameters file.

mz_name

[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'.

peptideprophet_analyzed

[pepXML output only] Write output in the format of a PeptideProphet analysis result. By default a 'raw' pepXML is produced that contains only search engine results.

score_type

[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit

ignore_proteins_per_peptide

[Sequest only] Workaround to deal with .out files that contain e.g. "+1" in references column, but do not list extra references in subsequent lines (try -debug 3 or 4)

scan_regex

[Mascot, pepXML, Percolator only] Regular expression used to extract the scan number or retention time. See documentation for details.

no_spectra_data_override

[+mz_file only] Avoid overriding 'spectra_data' in protein identifications if 'mz_file' is given and 'spectrum_reference's are added/updated. Use only if you are sure it is absolutely the same 'mz_file' as used for identification.

no_spectra_references_override

[+mz_file only] Avoid overriding 'spectrum_reference' in peptide identifications if 'mz_file' is given and a 'spectrum_reference' is already present.

add_ionmatch_annotation

[+mz_file only] Annotate the identifications with ion matches from spectra in 'mz_file' using the given tolerance (in Da). This will take quite some time.

concatenate_peptides

[FASTA output only] Will concatenate the top peptide hits to one peptide sequence, rather than write a new peptide for each hit.

number_of_hits

[FASTA output only] Controls how many peptide hits will be exported. A value of 0 or less exports all hits.

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)

isotope_model

Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks. Note that adding isotopic peaks is very slow.

max_isotope

Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'

max_isotope_probability

Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'

add_metainfo

Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++

add_losses

Adds common losses to those ion expect to have them, only water and ammonia loss is considered

sort_by_position

Sort output by position

add_precursor_peaks

Adds peaks of the unfragmented precursor ion to the spectrum

add_all_precursor_charges

Adds precursor peaks with all charges in the given range

add_abundant_immonium_ions

Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)

add_first_prefix_ion

If set to true e.g. b1 ions are added

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 (sometimes observed in CID and for some AAs in ExD due to H abstraction)

add_zp1_ions

Add peaks of z+1-radical cations (also [z+H]*^{+} or simply z*) to the spectrum (often observed in ExD)

add_zp2_ions

Add peaks of z+2-radical cations (also [z+2H]*^{2+} or simply z') to the spectrum (often observed in ExD esp. with higher precursor charges >3 and smaller z-ions.)

y_intensity

Intensity of the y-ions

b_intensity

Intensity of the b-ions

a_intensity

Intensity of the a-ions

c_intensity

Intensity of the c-ions

x_intensity

Intensity of the x-ions

z_intensity

Intensity of the z-ions

relative_loss_intensity

Intensity of loss ions, in relation to the intact ion intensity

precursor_intensity

Intensity of the precursor peak

precursor_H2O_intensity

Intensity of the H2O loss peak of the precursor

precursor_NH3_intensity

Intensity of the NH3 loss peak of the precursor

enzyme

Enzym used to digest the fasta proteins

missed_cleavages

Number of allowed missed cleavages while digesting the fasta proteins

min_charge

Minimum charge

max_charge

Maximum charge

precursor_charge

Manually set precursor charge. (default: 0, meaning max_charge + 1 will be used as precursor charge)

Views

IDFileConverter Std Output

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

IDFileConverter Error Output

The text sent to standard error during the execution of IDFileConverter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

• No workflows found

Links

• No links available

Developers