Identifies peptides in MS/MS spectra via Crux and tide-search.

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

Crux must be installed before this wrapper can be used. This should be the case for the installers.

The default parameters are set for a high resolution instrument. See the following publication:
Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. MacCoss and William Stafford Noble. "Rapid and accurate peptide identification from tandem mass spectra." Journal of Proteome Research. 7(7):3022-3027, 2008. doi: 10.1021/pr800127y

The command line parameters of this tool are:

CruxAdapter -- Identifies MS/MS spectra using Crux.
Full documentation: http://www.openms.de/documentation/TOPP_CruxAdapter.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.
To cite CruxAdapter:
  Park CI, Klammer AA, Käll L, MacCoss MJ, Noble WS. Rapid and accurate peptide identification from tandem mass spectra. J Proteome Res 7(7):3022-3027, 2008.. doi:10.1021/pr800127y.

Usage:
  CruxAdapter <options>

Options (mandatory options marked with '*'):
  -in <file>*                            Input file (valid formats: 'mzML')
  -out <file>*                           Output file (valid formats: 'idXML')
  -database <file>*                      FASTA file (valid formats: 'FASTA')
  -crux_executable <executable>*         Crux executable of the installation e.g. 'crux.exe'
  -extra_index_args <choice>             Extra arguments to be passed to tide-index
  -extra_search_args <choice>            Extra arguments to be passed to tide-search
  -extra_percolator_args <choice>        Extra arguments to be passed to percolator
  -precursor_mass_tolerance <tolerance>  Precursor monoisotopic mass tolerance (Crux parameter: peptide_mass_
                                         tolerance) (default: '10.0')
  -precursor_mass_units <choice>         Unit of precursor mass tolerance (amu, m/z or ppm) (default: 'ppm' 
                                         valid: 'mass', 'mz', 'ppm')
  -fragment_bin_offset <offset>          In the discretization of the m/z axes of the observed and theoretica
                                         l spectra, this parameter specifies the location of the left edge
                                         of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx
                                         means the left edge of the first bin will be located at +0.xx Da).
                                         (default: '0.0')
  -fragment_bin_width <width>            Before calculation of the XCorr score, the m/z axes of the observed 
                                         and theoretical spectra are discretized. This parameter specifies
                                         the size of each bin. The exact formula for computing the discretize
                                         d m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where
                                         x is the observed m/z value. For low resolution ion trap ms/ms data
                                         1.0005079 and for high resolution ms/ms 0.02 is recommended. (defaul
                                         t: '0.02')
  -isotope_error <choice>                List of positive, non-zero integers.
  -run_percolator <true/false>           Whether to run percolator after tide-search (default: 'true' valid: 
                                         'true', 'false')
  -enzyme <cleavage site>                The enzyme used for peptide digestion. (default: 'trypsin' valid: 
                                         'custom-enzyme', 'arg-c', 'no-enzyme', 'staph-protease', 'proline-en
                                         dopeptidase', 'glu-c', 'pepsin-a', 'cyanogen-bromide', 'clostripain'
                                         , 'elastase-trypsin-chymotrypsin', 'trypsin', 'iodosobenzoate', 'try
                                         psin/p', 'lys-c', 'lys-n', 'elastase', 'asp-n', 'chymotrypsin')
  -digestion <choice>                    Full, partial or non specific digestion (default: 'full-digest' vali
                                         d: 'full-digest', 'partial-digest', 'non-specific-digest')
  -allowed_missed_cleavages <num>        Number of possible cleavage sites missed by the enzyme, maximum valu
                                         e is 5; for enzyme search (default: '0')
  -decoy-format <choice>                 Decoy generation method either by reversing the sequence or shufflin
                                         g it. (default: 'shuffle' valid: 'none', 'shuffle', 'peptide-reverse
                                         ', 'protein-reverse')
  -keep-terminal-aminos <choice>         Whether to keep N and C terminal in place or also shuffled / reverse
                                         d. (default: 'NC' valid: 'N', 'C', 'NC', 'none')
  -cterm_modifications <mods>            Specifies C-terminal static and variable mass modifications on pepti
                                         des.  Specify a comma-separated list of C-terminal modification sequ
                                         ences of the form: X+21.9819 Default = <empty>.
  -nterm_modifications <mods>            Specifies N-terminal static and variable mass modifications on pepti
                                         des.  Specify a comma-separated list of N-terminal modification sequ
                                         ences of the form: 1E-18.0106,C-17.0265 Default = <empty>.
  -modifications <mods>                  Expression for static and variable mass modifications to include. 
                                         Specify a comma-separated list of modification sequences of the form
                                         : C+57.02146,2M+15.9949,1STY+79.966331,... Default = C+57.02146.
  -test_fdr <fdr>                        False discovery rate threshold used in selecting hyperparameters 
                                         during internal cross-validation and for reporting the final results
                                         . (default: '0.01')
  -train_fdr <fdr>                       False discovery rate threshold to define positive examples in traini
                                         ng. (default: '0.01')
                                         
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 (defa
                                         ult: '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

+CruxAdapterIdentifies MS/MS spectra using Crux.

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

++1Instance '1' section for 'CruxAdapter'

in Input fileinput file*.mzML

out Output fileoutput file*.idXML

database FASTA fileinput file*.FASTA

crux_executablecrux Crux executable of the installation e.g. 'crux.exe'input file

extra_index_args Extra arguments to be passed to tide-index

extra_search_args Extra arguments to be passed to tide-search

extra_percolator_args Extra arguments to be passed to percolator

precursor_mass_tolerance10.0 Precursor monoisotopic mass tolerance (Crux parameter: peptide_mass_tolerance)

precursor_mass_unitsppm Unit of precursor mass tolerance (amu, m/z or ppm)mass,mz,ppm

fragment_bin_offset0.0 In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da).

fragment_bin_width0.02 Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended.

isotope_error List of positive, non-zero integers.

run_percolatortrue Whether to run percolator after tide-searchtrue,false

enzymetrypsin The enzyme used for peptide digestion.custom-enzyme,arg-c,no-enzyme,staph-protease,proline-endopeptidase,glu-c,pepsin-a,cyanogen-bromide,clostripain,elastase-trypsin-chymotrypsin,trypsin,iodosobenzoate,trypsin/p,lys-c,lys-n,elastase,asp-n,chymotrypsin

digestionfull-digest Full, partial or non specific digestionfull-digest,partial-digest,non-specific-digest

allowed_missed_cleavages0 Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search

custom_enzyme Specify rules for in silico digestion of protein sequences. Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site.

decoy_prefixdecoy_ Specifies the prefix of the protein names that indicate a decoy

decoy-formatshuffle Decoy generation method either by reversing the sequence or shuffling it.none,shuffle,peptide-reverse,protein-reverse

keep-terminal-aminosNC Whether to keep N and C terminal in place or also shuffled / reversed.N,C,NC,none

cterm_modifications Specifies C-terminal static and variable mass modifications on peptides. Specify a comma-separated list of C-terminal modification sequences of the form: X+21.9819 Default = .

nterm_modifications Specifies N-terminal static and variable mass modifications on peptides. Specify a comma-separated list of N-terminal modification sequences of the form: 1E-18.0106,C-17.0265 Default = .

modifications Expression for static and variable mass modifications to include. Specify a comma-separated list of modification sequences of the form: C+57.02146,2M+15.9949,1STY+79.966331,... Default = C+57.02146.

test_fdr0.01 False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results.

train_fdr0.01 False discovery rate threshold to define positive examples in training.

deisotopefalse Deisotope spectra before searchingtrue,false

report_decoysfalse Include decoys in the final reported datasettrue,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