Identifies peptides in MS/MS spectra via Inspect.

pot. predecessor tools	$\longrightarrow$ InspectAdapter $\longrightarrow$	pot. successor tools
any signal-/preprocessing tool (in mzML format)	$\longrightarrow$ InspectAdapter $\longrightarrow$	IDFilter or any protein/peptide processing tool

Experimental classes:: This tool has not been tested thoroughly and might behave not as expected!

This wrapper application serves for getting peptide peptide_identifications for MS/MS spectra. The wrapper can be executed in three different modes:

The whole process of ProteinIdentification via Inspect is executed. Inputfile is an mz file containing the MS/MS spectra (Supported spectrum file formats are .mzXML, .mzData) for which the identifications are to be found and one ore more databases in either trie, FASTA or Swissprot format containing the possible proteins. The given databases are converted and merged into one trie database. This is done because Inspect does the conversion anyway (though with a bug) and may actually not use more than two databases (one of them in trie format). Additionally you thus can reuse the database without having Inspect done the conversion every time. The drawback is, of course, that you need the same amount of space for the trie database as well, which can, in case of large and/or many databases, be a problem. The results are written as a idXML output file. This mode is selected by default.
Only the first part of the ProteinIdentification process is performed. This means that an Inspect input file is generated and the given databases are converted and merged into one trie database. This file can be used directly with Inspect whereas the created database and the spectrum file(s) have to remain at the given positions. Calling an Inspect process should look like the following:

./inspect -i inputfilename -o outputfilename

Consult your Inspect reference manual for further details.

This mode is selected by the -inspect_in option in the command line.
Only the second part of the ProteinIdentification process is performed. This means that the output of an Inspect run is analyzed and the result written to an idXML file.

This mode is selected by the -inspect_out option in the command line.

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:

InspectAdapter -- Annotates MS/MS spectra using Inspect.
Full documentation: http://www.openms.de/documentation/TOPP_InspectAdapter.html
Version: 2.5.0-nightly-2020-03-06 Mar  7 2020, 01:22:16, Revision: 84b1398
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  InspectAdapter <options>

Options (mandatory options marked with '*'):
  -in <file>*                      Input file in mzXML or mzData format.
                                   Note: In mode 'inspect_out' an Inspect results file is read. (valid forma
                                   ts: 'mzXML', 'mzData')
  -out <file>*                     Output file in idXML format.
                                   Note: In mode 'inspect_in' an Inspect input file is written. (valid forma
                                   ts: 'idXML')
  -inspect_in                      If this flag is set the InspectAdapter will read in mzXML,
                                   write an Inspect input file and generate a trie database
  -inspect_out                     If this flag is set the InspectAdapter will read in a Inspect results file
                                   and write idXML
  -inspect_directory <dir>         The directory in which Inspect is located
  -temp_data_directory <dir>       A directory in which some temporary files can be stored
  -dbs <file>                      Name(s) of database(s) to search in (FASTA and SwissProt supported)
  -trie_dbs <file>                 Name(s) of databases(s) to search in (trie-format)
  -new_db <file>                   Name of the merged trie database
  -instrument <i>                  The instrument that was used to measure the spectra
                                   (If set to QTOF, uses a QTOF-derived fragmentation model,
                                   and does not attempt to correct the parent mass.) (valid: 'ESI-ION-TRAP',
                                   'QTOF', 'FT-Hybrid')
  -precursor_mass_tolerance <tol>  The precursor mass tolerance (default: '2.0')
  -peak_mass_tolerance <tol>       The peak mass tolerance (default: '1.0')
  -list_modifications              Show a list of the available modifications
  -modifications <mods>            The colon-separated modifications; may be
                                   <name>,<type>, e.g.: Deamidation,opt or
                                   <composition>,<residues>,<type>,<name>, e.g.: H2C2O,KCS,opt,Acetyl or
                                   <mass>,<residues>,<type>,<name>, e.g.: 42.0367,KCS,opt,Acetyl or
                                   Valid values for type are "fix" and "opt" (default)
                                   If you want terminal PTMs, write "cterm" or "nterm" instead of residues
  -use_monoisotopic_mod_mass       Use monoisotopic masses for the modifications
  -modifications_xml_file <file>   Name of an XML file with the modifications
  -cleavage <enz>                  The enzyme used for digestion (default: 'Trypsin')
  -inspect_output <file>           Name for the output file of Inspect (may only be used in a full run)
  -inspect_input <file>            Name for the input file of Inspect (may only be used in a full run)
  -multicharge                     Attempt to guess the precursor charge and mass,
                                   and consider multiple charge states if feasible
  -max_modifications_pp <num>      Number of PTMs permitted in a single peptide. (default: '-1')
  -tag_count <num>                 Number of tags to generate (default: '-1')
  -no_tmp_dbs                      No temporary databases are used
  -p_value <prob>                  Annotations with inferior p-value are ignored (default: '1.0')

Options for blind search:
  -blind:blind                     Perform a blind search (allowing arbitrary modification masses),
                                   is preceeded by a normal search to gain a smaller database.
                                   (in full mode only)
  -blind:blind_only                Like blind but no prior search is performed to reduce the database size
  -blind:p_value_blind <prob>      Used for generating the minimized database (default: '1.0')
  -blind:snd_db <file>             Name of the minimized trie database generated when using blind mode.
  -blind:max_ptm_size <num>        Maximum modification size (in Da) to consider (default: '250.0')

                                   
  -contact_name <name>             Name of the contact (default: 'unknown')
  -contact_institution <name>      Name of the contact institution (default: 'unknown')
  -contact_info <info>             Some information about the contact (default: 'unknown')
                                   
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

+InspectAdapterAnnotates MS/MS spectra using Inspect.

version2.5.0-nightly-2020-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'InspectAdapter'

in input file in mzXML or mzData format.
Note: In mode 'inspect_out' an Inspect results file is read.input file*.mzXML,*.mzData

out output file in idXML format.
Note: In mode 'inspect_in' an Inspect input file is written.output file*.idXML

inspect_infalse if this flag is set the InspectAdapter will read in mzXML,
write an Inspect input file and generate a trie databasetrue,false

inspect_outfalse if this flag is set the InspectAdapter will read in a Inspect results file
and write idXMLtrue,false

inspect_directory the directory in which Inspect is located

temp_data_directory a directory in which some temporary files can be stored

dbs name(s) of database(s) to search in (FASTA and SwissProt supported)

trie_dbs name(s) of databases(s) to search in (trie-format)

new_db name of the merged trie database

instrument the instrument that was used to measure the spectra
(If set to QTOF, uses a QTOF-derived fragmentation model,
and does not attempt to correct the parent mass.)ESI-ION-TRAP,QTOF,FT-Hybrid

precursor_mass_tolerance2.0 the precursor mass tolerance

peak_mass_tolerance1.0 the peak mass tolerance

list_modificationsfalse show a list of the available modificationstrue,false

modifications the colon-separated modifications; may be
,, e.g.: Deamidation,opt or
,,,, e.g.: H2C2O,KCS,opt,Acetyl or
,,,, e.g.: 42.0367,KCS,opt,Acetyl or
Valid values for type are "fix" and "opt" (default)
If you want terminal PTMs, write "cterm" or "nterm" instead of residues

use_monoisotopic_mod_massfalse use monoisotopic masses for the modificationstrue,false

modifications_xml_file name of an XML file with the modifications

cleavageTrypsin the enzyme used for digestion

inspect_output name for the output file of Inspect (may only be used in a full run)output file

inspect_input name for the input file of Inspect (may only be used in a full run)input file

multichargefalse attempt to guess the precursor charge and mass,
and consider multiple charge states if feasibletrue,false

max_modifications_pp-1 number of PTMs permitted in a single peptide.

tag_count-1 number of tags to generate

no_tmp_dbsfalse no temporary databases are usedtrue,false

p_value1.0 annotations with inferior p-value are ignored

contact_nameunknown Name of the contact

contact_institutionunknown Name of the contact institution

contact_infounknown Some information about the contact

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

+++blindOptions for blind search

blindfalse perform a blind search (allowing arbitrary modification masses),
is preceeded by a normal search to gain a smaller database.
(in full mode only)true,false

blind_onlyfalse like blind but no prior search is performed to reduce the database sizetrue,false

p_value_blind1.0 used for generating the minimized database

snd_db name of the minimized trie database generated when using blind mode.

max_ptm_size250.0 maximum modification size (in Da) to consider

Todo:: rewrite the Adapter! It uses old formats and coding style, e.g. mzData input allowed, no input restrictions, manual (unneccessary file checking of input files) etc... + the interface is not convenient, etc ...