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PILISIdentification

Performs an ProteinIdentification with PILIS

Experimental classes:
This TOPP-tool is not well tested and not all features might be properly implemented and tested!
pot. predecessor tools $ \longrightarrow $ PILISIdentification $ \longrightarrow $ pot. successor tools
PILISModelTrainer ConsensusID
IDMapper

The PILISIdentification TOPP tool performs a ProteinIdentification run with the PILIS ProteinIdentification engine. As input the file given in the in parameters is used. The identifications are written into an idXML file given in the out parameter. Additionally the model_file must be specified. To perform a search also a peptide database file should be used,given in the peptide_db_file parameter. This should contain a peptide in a separate line, either only the sequence or additionally with weight and charge in the second and third column.

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

PILISIdentification -- performs a peptide/protein identification with the PILIS engine
Version: 2.0.0 Aug 25 2015, 00:02:58, Revision: GIT-NOTFOUND

Usage:
  PILISIdentification <options>

Options (mandatory options marked with '*'):
  -in <file>*                                        Input file in MzML format (valid formats: 'mzML')
  -out <file>*                                       Output file in idXML format (valid formats: 'idXML')
  -model_file <file*                                 The model file of the PILISModel
  -peptide_db_file <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 fil
                                                     e
                                                     may contain only peptide sequences each in a separate l
                                                     ine
                                                     repectively
  -precursor_mass_tolerance <tol>                    The precursor mass tolerance (default: '2')
  -peak_mass_tolerance <tol>                         The peak mass tolerance (default: '1')
  -max_pre_candidates <int>                          Number of candidates that are used for precise scoring 
                                                     (default: '200')
  -max_candidates <int>                              Number of candidates that are reported by PILIS (default
                                                     : '20')
  -upper_mz <double>                                 Upper mz interval endpoint (default: '2000')
  -lower_mz <double>                                 Lower mz interval endpoint (default: '200')
  -fixed_modifications <mods>                        Monoisotopic_mass@residues e.g.: 57.021464@C
                                                     

Parameters of PILISModel:
  -model:charge_directed_threshold <double>          Bla (default: '0.3')
  -model:charge_remote_threshold <double>            Bla (default: '0.2')
  -model:charge_loss_factor <double>                 Bla (default: '0.5')
  -model:min_y_ion_intensity <double>                 (default: '0.2')
  -model:min_b_ion_intensity <double>                 (default: '0.15')
  -model:min_a_ion_intensity <double>                 (default: '0.05')
  -model:min_y_loss_intensity <double>                (default: '0.05')
  -model:min_b_loss_intensity <double>                (default: '0.02')
  -model:visible_model_depth <int>                   Bla (default: '30')
  -model:model_depth <int>                           Bla (default: '4')

                                                     

Parameters of PILISScoring:
  -scoring:use_local_scoring                         ...
  -scoring:do_not_use_evalue_scoring                 ...
  -scoring:survival_function_bin_size <int>          ... (default: '20')
  -scoring:global_linear_fitting_threshold <double>  ... (default: '0.1')
  -scoring:local_linear_fitting_threshold <double>   ... (default: '0.5')

                                                     
                                                     
Common TOPP options:
  -ini <file>                                        Use the given TOPP INI file
  -threads <n>                                       Sets the number of threads allowed to be used by the 
                                                     TOPP tool (default: '1')
  -write_ini <file>                                  Writes the default configuration file
  --help                                             Shows options
  --helphelp                                         Shows all options (including advanced)

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+PILISIdentificationperforms a peptide/protein identification with the PILIS engine
version2.0.0 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
repectively
input 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
forcefalse Overwrite tool specific checks.true,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 ...
Todo:
Check for missing precursors (Hiwi)

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:56 using doxygen 1.8.9.1