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required parameter

advanced parameter

+InspectAdapterAnnotates MS/MS spectra using Inspect.

version1.10.0 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 the precursor mass tolerance

peak_mass_tolerance1 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 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

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 used for generating the minimized database

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

max_ptm_size250 maximum modification size (in Da) to consider