Legend:
required parameter
advanced parameter
+PILISIdentificationperforms a peptide/protein identification with the PILIS engine
version1.10.0
Version of the tool that generated this parameters file.
++1Instance '1' section for 'PILISIdentification'
in
input file in MzML formatinput file*.mzML
out
output file in idXML formatoutput file*.idXML
model_file
the model file of the PILISModelinput file
peptide_db_file
a file which should contain peptides in the format
DFPIANGER 1019.09 1
where the first column is the peptide, the second the m/z
the third the charge. As a alternative the sequence file
may contain only peptide sequences each in a separate line
repectivelyinput file
precursor_mass_tolerance2
the precursor mass tolerance
peak_mass_tolerance1
the peak mass tolerance
max_pre_candidates200
number of candidates that are used for precise scoring
max_candidates20
number of candidates that are reported by PILIS
upper_mz2000
upper mz interval endpoint
lower_mz200
lower mz interval endpoint
fixed_modifications
monoisotopic_mass@residues e.g.: 57.021464@C
log
Name of log file (created only when specified)
debug0
Sets the debug level
threads1
Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse
Disables progress logging to command linetrue,false
testfalse
Enables the test mode (needed for internal use only)true,false
+++modelParameters of PILISModel
charge_directed_threshold0.3
bla
charge_remote_threshold0.2
bla
charge_loss_factor0.5
bla
min_y_ion_intensity0.2
min_b_ion_intensity0.15
min_a_ion_intensity0.05
min_y_loss_intensity0.05
min_b_loss_intensity0.02
visible_model_depth30
bla
model_depth4
bla
+++scoringParameters of PILISScoring
use_local_scoringfalse
...true,false
do_not_use_evalue_scoringfalse
...true,false
survival_function_bin_size20
...
global_linear_fitting_threshold0.1
...
local_linear_fitting_threshold0.5
...