ProteinInference

Computes a protein identification based on the number of identified peptides.

pot. predecessor tools	$\longrightarrow$ ProteinInterference $\longrightarrow$	pot. successor tools
MascotAdapter (or other ID engines)		PeptideIndexer
FalseDiscoveryRate
IDFilter

Experimental classes:: This TOPP-tool is not well tested and not all features might be properly implemented and tested!

This tool counts the peptide sequences that match a protein accession. From this count for all protein hits in the respective id run, only those proteins are accepted that have at least a given number of peptides sequences identified. The peptide identifications should be prefiltered with respect to false discovery rate and the score in general to remove bad identifications.

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:

ProteinInference -- Protein inference based on the number of identified peptides.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  ProteinInference <options>

Options (mandatory options marked with '*'):
  -in <file>*                               Input file (valid formats: 'idXML')
  -out <file>*                              Output file (valid formats: 'idXML')
                                            
  -min_peptides_per_protein <num>           Minimal number of peptides needed for a protein identification 
                                            (default: '2' min: '1')
  -treat_charge_variants_separately         If this flag is set, different charge variants of the same peptid
                                            e sequence count as inidividual evidences.
  -treat_modification_variants_separately   If this flag is set, different modification variants of the same 
                                            peptide sequence count as individual evidences.
                                            
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

+ProteinInferenceProtein inference based on the number of identified peptides.

version2.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'ProteinInference'

in input fileinput file*.idXML

out output fileoutput file*.idXML

min_peptides_per_protein2 Minimal number of peptides needed for a protein identification1:∞

treat_charge_variants_separatelyfalse If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences.true,false

treat_modification_variants_separatelyfalse If this flag is set, different modification variants of the same peptide sequence count as individual evidences.true,false

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