Novoradapter for de novo sequencing from tandem mass spectrometry data.

pot. predecessor tools	→ NovorAdapter →	pot. successor tools
signal-/preprocessing e.g. FileFilter (in mzML format)	→ NovorAdapter →	IDFilter or any protein/peptide processing tool

This tool can be used for de novo sequencing of peptides from MS/MS data.

Novor must be installed before this wrapper can be used. This wrapper was successfully tested with version v1.06.0634 (stable).

Novor settings can be either used via command line or directly using a param file (param.txt).

Parameter names have been changed to match names found in other search engine adapters. For further information check the Novor wiki (http://wiki.rapidnovor.com/wiki/Main_Page) and the official tool website (https://www.rapidnovor.com/).

The command line parameters of this tool are:

NovorAdapter -- Performs de novo sequencing of peptides from MS/MS data with Novor.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_NovorAdapter.html
Version: 3.3.0-pre-nightly-2024-11-20 Nov 21 2024, 02:34:56, Revision: decb5c8
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
To cite NovorAdapter:
 + Ma Bin. Novor: Real-Time Peptide de Novo Sequencing Software. Journal of The American Society for Mass 
   Spectrometry; 30 June 2015. doi:10.1007/s13361-015-1204-0.

Usage:
  NovorAdapter <options>

Options (mandatory options marked with '*'):
  -executable <jar>                   Novor.jar
  -in <file>*                         MzML Input file (valid formats: 'mzML')
  -out <file>*                        Novor idXML output (valid formats: 'idXML')
  -enzyme <choice>                    Digestion enzyme - currently only Trypsin is supported  (default: 'Tryp
                                      sin') (valid: 'Trypsin')
  -fragmentation <choice>             Fragmentation method (default: 'CID') (valid: 'CID', 'HCD')
  -massAnalyzer <choice>              MassAnalyzer e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF) (def
                                      ault: 'Trap') (valid: 'Trap', 'TOF', 'FT')
  -fragment_mass_tolerance <double>   Fragmentation error tolerance  (Da) (default: '0.5')
  -precursor_mass_tolerance <double>  Precursor error tolerance  (ppm or Da) (default: '15.0')
  -precursor_error_units <choice>     Unit of precursor mass tolerance (default: 'ppm') (valid: 'ppm', 'Da')
  -variable_modifications <mods>      Variable modifications (valid: 'Acetyl (K)', 'Acetyl (N-term)', 'Amidat
                                      ed (C-term)', 'Ammonia-loss (N-term C)', 'Biotin (K)', 'Biotin (N-term)
                                      ', 'Carbamidomethyl (C)', 'Carbamyl (K)', 'Carbamyl (N-term)', 'Carboxy
                                      methyl (C)', 'Deamidated (NQ)', 'Dehydrated (N-term C)', 'Dioxidation 
                                      (M)', 'Methyl (C-term)', 'Methyl (DE)', 'Oxidation (M)', 'Oxidation 
                                      (HW)', 'Phospho (ST)', 'Phospho (Y)', 'Pyro-carbamidomethyl (N-term 
                                      C)', 'Pyro-Glu (E)', 'Pyro-Glu (Q)', 'Sodium (C-term)', 'Sodium (DE)', 
                                      'Sulfo (STY)', 'Trimethyl (RK)')
  -fixed_modifications <mods>         Fixed modifications (valid: 'Acetyl (K)', 'Acetyl (N-term)', 'Amidated 
                                      (C-term)', 'Ammonia-loss (N-term C)', 'Biotin (K)', 'Biotin (N-term)', 
                                      'Carbamidomethyl (C)', 'Carbamyl (K)', 'Carbamyl (N-term)', 'Carboxymet
                                      hyl (C)', 'Deamidated (NQ)', 'Dehydrated (N-term C)', 'Dioxidation (M)'
                                      , 'Methyl (C-term)', 'Methyl (DE)', 'Oxidation (M)', 'Oxidation (HW)', 
                                      'Phospho (ST)', 'Phospho (Y)', 'Pyro-carbamidomethyl (N-term C)', 'Pyro
                                      -Glu (E)', 'Pyro-Glu (Q)', 'Sodium (C-term)', 'Sodium (DE)', 'Sulfo 
                                      (STY)', 'Trimethyl (RK)')
  -forbiddenResidues <mods>           Forbidden Resiudes (valid: 'I', 'U')
  -novorFile <file>                   File to introduce customized algorithm parameters for advanced users 
                                      (otional .novor file) (valid formats: 'novor')
  -java_executable <file>             The Java executable. Usually Java is on the system PATH. If Java is 
                                      not found, use this parameter to specify the full path to Java
  -java_memory <num>                  Maximum Java heap size (in MB) (default: '3500')
                                      
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

+NovorAdapterPerforms de novo sequencing of peptides from MS/MS data with Novor.

version3.3.0-pre-nightly-2024-11-20 Version of the tool that generated this parameters file.

++1Instance '1' section for 'NovorAdapter'

executablenovor.jar novor.jarinput file

in MzML Input fileinput file*.mzML

out Novor idXML outputoutput file*.idXML

enzymeTrypsin Digestion enzyme - currently only Trypsin is supported Trypsin

fragmentationCID Fragmentation methodCID, HCD

massAnalyzerTrap MassAnalyzer e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)Trap, TOF, FT

fragment_mass_tolerance0.5 Fragmentation error tolerance (Da)

precursor_mass_tolerance15.0 Precursor error tolerance (ppm or Da)

precursor_error_unitsppm Unit of precursor mass toleranceppm, Da

variable_modifications[] Variable modificationsAcetyl (K), Acetyl (N-term), Amidated (C-term), Ammonia-loss (N-term C), Biotin (K), Biotin (N-term), Carbamidomethyl (C), Carbamyl (K), Carbamyl (N-term), Carboxymethyl (C), Deamidated (NQ), Dehydrated (N-term C), Dioxidation (M), Methyl (C-term), Methyl (DE), Oxidation (M), Oxidation (HW), Phospho (ST), Phospho (Y), Pyro-carbamidomethyl (N-term C), Pyro-Glu (E), Pyro-Glu (Q), Sodium (C-term), Sodium (DE), Sulfo (STY), Trimethyl (RK)

fixed_modifications[] Fixed modificationsAcetyl (K), Acetyl (N-term), Amidated (C-term), Ammonia-loss (N-term C), Biotin (K), Biotin (N-term), Carbamidomethyl (C), Carbamyl (K), Carbamyl (N-term), Carboxymethyl (C), Deamidated (NQ), Dehydrated (N-term C), Dioxidation (M), Methyl (C-term), Methyl (DE), Oxidation (M), Oxidation (HW), Phospho (ST), Phospho (Y), Pyro-carbamidomethyl (N-term C), Pyro-Glu (E), Pyro-Glu (Q), Sodium (C-term), Sodium (DE), Sulfo (STY), Trimethyl (RK)

forbiddenResidues[] Forbidden ResiudesI, U

novorFile File to introduce customized algorithm parameters for advanced users (otional .novor file)input file*.novor

java_executablejava The Java executable. Usually Java is on the system PATH. If Java is not found, use this parameter to specify the full path to Javainput file

java_memory3500 Maximum Java heap size (in MB)

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 Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false