Peptide Identification with MSFragger

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

MSFragger must be installed before this adapter can be used.

All MSFragger parameters (as specified in the fragger.params file) have been transcribed to parameters of this OpenMS util. It is not possible to provide an explicit fragger.params file to avoid redundancy with the ini file. This adapter creates an fragger.params file prior to calling MSFragger. If the fragger.params file should be inspected, set the -debug option to 2. MSFraggerAdapter will print the path to the working directory to standard out.

MSFragger can process multiple input files (mzML, mzXML) one after another. The number of output files specified must match the number of input spectra files. The output file is then matched to the input file by index. The default parameters of the adapter are the same as given by the official MSFragger manual.

Please cite: Andy T Kong, Felipe V Leprevost, Dmitry M Avtonomov, Dattatreya Mellacheruvu & Alexey I Nesvizhskii MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics Nature Methods volume 14, pages 513–520 (2017) doi:10.1038/nmeth.4256

The command line parameters of this tool are:

MSFraggerAdapter -- Peptide Identification with MSFragger.
Important note:
The Regents of the University of Michigan (“Michigan”) grants us permission to redistribute
the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available
for use on related service offerings supported by the University of Tubingen and the Center for
Integrative Bioinformatics.
Per the license agreement the use of the pipeline and associated materials is for academic
research, non-commercial or educational purposes. Any commercial use inquiries
...

Full documentation: http://www.openms.de/doxygen/release/2.7.0/html/UTILS_MSFraggerAdapter.html
Version: 2.7.0 Sep 13 2021, 20:58:47, Revision: 9110e58
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 MSFraggerAdapter:
  Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature Methods volume 14, pages 513–520 (2017). doi:doi:10.1038/nmeth.4256.

Usage:
  MSFraggerAdapter <options>

Options (mandatory options marked with '*'):
  -license <license>*                                                      Set to yes, if you have read and 
                                                                           agreed to the MSFragger license
                                                                           terms. (valid: 'yes', 'no')
  -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_heapmemory <num>                                                   Maximum Java heap size (in MB) 
                                                                           (default: '3500')
  -executable <path_to_executable>                                         Path to the MSFragger executable 
                                                                           to use; may be empty if the execut
                                                                           able is globally available.
  -in <file>*                                                              Input File with specta for MSFragg
                                                                           er (valid formats: 'mzML', 'mzXML'
                                                                           )
  -out <file>*                                                             MSFragger output file (valid forma
                                                                           ts: 'idXML')
  -opt_out <file>                                                          MSFragger optional output file 
                                                                           (valid formats: 'pepXML')
  -database <path_to_fasta>*                                               Protein FASTA database file path 
                                                                           (valid formats: 'FASTA', 'fasta',
                                                                           'fa', 'fas')

Search Tolerances:
  -tolerance:precursor_mass_tolerance_lower <precursor_mass_tolerance>     Lower precursor mass tolerance 
                                                                           (default: '20.0' min: '0.0')
  -tolerance:precursor_mass_tolerance_upper <precursor_mass_tolerance>     Upper precursor mass tolerance 
                                                                           (default: '20.0' min: '0.0')
  -tolerance:precursor_mass_unit <precursor_mass_unit>                     Unit of precursor mass tolerance 
                                                                           (default: 'ppm' valid: 'Da', 'ppm'
                                                                           )
  -tolerance:precursor_true_tolerance <precursor_true_tolerance>           True precursor mass tolerance (win
                                                                           dow is +/- this value). Used for
                                                                           tie breaker of results (in spectra
                                                                           lly ambiguous cases) and zero bin
                                                                           boosting in open searches (0 disab
                                                                           les these features). This option
                                                                           is STRONGLY recommended for open
                                                                           searches. (default: '0.0' min:
                                                                           '0.0')
  -tolerance:precursor_true_unit <precursor_true_unit>                     Unit of precursor true tolerance 
                                                                           (default: 'ppm' valid: 'Da', 'ppm'
                                                                           )
  -tolerance:fragment_mass_tolerance <fragment_mass_tolerance>             Fragment mass tolerance (window 
                                                                           is +/- this value) (default: '20.0
                                                                           ' min: '0.0')
  -tolerance:fragment_mass_unit <fragment_mass_unit>                       Unit of fragment mass tolerance 
                                                                           (default: 'ppm' valid: 'Da', 'ppm'
                                                                           )
  -tolerance:isotope_error <isotope_error>                                 Isotope correction for MS/MS event
                                                                           s triggered on isotopic peaks.
                                                                           Should be set to 0 (disabled) for
                                                                           open search or 0/1/2 for correctio
                                                                           n of narrow window searches. Shift
                                                                           s the precursor mass window to
                                                                           multiples of this value multiplied
                                                                           by the mass of C13-C12. (default:
                                                                           '0' valid: '0', '1', '2')

In-Silico Digestion Parameters:
  -digest:search_enzyme_name <search_enzyme_name>                          Name of the enzyme to be written 
                                                                           to the pepXML file (default: 'Tryp
                                                                           sin' valid: 'Arg-C/P', 'Asp-N',
                                                                           'Asp-N/B', 'Asp-N_ambic', 'Chymotr
                                                                           ypsin', 'Chymotrypsin/P', 'CNBr',
                                                                           'Formic_acid', 'Lys-C', 'Lys-N',
                                                                           'Lys-C/P', 'PepsinA', 'TrypChymo',
                                                                           'Trypsin/P', 'V8-DE', 'V8-E',
                                                                           ...
                                                                           ic cleavage')
  -digest:search_enzyme_cutafter <search_enzyme_cutafter>                  Residues after which the enzyme 
                                                                           cuts (specified as a string of
                                                                           amino acids) (default: 'KR')
  -digest:search_enzyme_nocutbefore <search_enzyme_nocutbefore>            Residues that the enzyme will not 
                                                                           cut before (default: 'P')
  -digest:num_enzyme_termini <num_enzyme_termini>                          Number of enzyme termini (non-enzy
                                                                           matic (0), semi (1), fully (2)
                                                                           (default: 'fully' valid: 'non-enzy
                                                                           matic', 'semi', 'fully')
  -digest:allowed_missed_cleavage <allowed_missed_cleavage>                Allowed number of missed cleavages
                                                                           (default: '2' valid: '0', '1',
                                                                           '2', '3', '4', '5')
  -digest:min_length <digest_min_length>                                   Minimum length of peptides to be 
                                                                           generated during in-silico digesti
                                                                           on (default: '7' min: '0')
  -digest:max_length <digest_max_length>                                   Maximum length of peptides to be 
                                                                           generated during in-silico digesti
                                                                           on (default: '64' min: '0')
  -digest:mass_range_min <digest_mass_range_min>                           Min mass of peptides to be generat
                                                                           ed (Da) (default: '500.0' min:
                                                                           '0.0')
  -digest:mass_range_max <digest_mass_range_max>                           Max mass of peptides to be generat
                                                                           ed (Da) (default: '5000.0' min:
                                                                           '0.0')

Variable Modification Parameters:
  -varmod:clip_nterm_m                                                     Specifies the trimming of a protei
                                                                           n N-terminal methionine as a varia
                                                                           ble modification
  -varmod:masses <varmod1_mass .. varmod7_mass>                            Masses for variable modifications
  -varmod:syntaxes <varmod1_syntax .. varmod7_syntax>                      Syntax Strings for variable modifi
                                                                           cations
  -varmod:enable_common                                                    Enable common variable modificatio
                                                                           ns (15.9949 M and 42.0106 [^)
  -varmod:not_allow_multiple_variable_mods_on_residue                      Do not allow any one amino acid 
                                                                           to be modified by multiple variabl
                                                                           e modifications
  -varmod:max_variable_mods_per_mod <max_variable_mods_per_mod>            Maximum number of residues that 
                                                                           can be occupied by each variable
                                                                           modification (default: '2' valid:
                                                                           '0', '1', '2', '3', '4', '5')
  -varmod:max_variable_mods_combinations <max_variable_mods_combinations>  Maximum allowed number of modified
                                                                           variably modified peptides from
                                                                           each peptide sequence, (maximum
                                                                           of 65534). If a greater number
                                                                           than the maximum is generated,
                                                                           only the unmodified peptide is
                                                                           considered (default: '5000' min:
                                                                           '0' max: '65534')

Spectrum Processing Parameters:
  -spectrum:minimum_peaks <minimum_peaks>                                  Minimum number of peaks in experim
                                                                           ental spectrum for matching (defau
                                                                           lt: '10' min: '0')
  -spectrum:use_topn_peaks <use_topN_peaks>                                Pre-process experimental spectrum 
                                                                           to only use top N peaks (default:
                                                                           '50' min: '0')
  -spectrum:minimum_ratio <minimum_ratio>                                  Filters out all peaks in experimen
                                                                           tal spectrum less intense than
                                                                           this multiple of the base peak
                                                                           intensity (default: '0.0' min:
                                                                           '0.0' max: '1.0')
  -spectrum:clear_mz_range_min <clear_mz_range_min>                        Removes peaks in this m/z range 
                                                                           prior to matching (minimum value).
                                                                           Useful for iTRAQ/TMT experiments
                                                                           (i.e. 0.0 150.0) (default: '0.0'
                                                                           min: '0.0')
  -spectrum:clear_mz_range_max <clear_mz_range_max>                        Removes peaks in this m/z range 
                                                                           prior to matching (maximum value).
                                                                           Useful for iTRAQ/TMT experiments
                                                                           (i.e. 0.0 150.0) (default: '0.0'
                                                                           min: '0.0')
  -spectrum:max_fragment_charge <max_fragment_charge>                      Maximum charge state for theoretic
                                                                           al fragments to match (default:
                                                                           '2' valid: '1', '2', '3', '4')
  -spectrum:override_charge                                                Ignores precursor charge and uses 
                                                                           charge state specified in precurso
                                                                           r_charge range (parameters: spectr
                                                                           um:precursor_charge_min and spectr
                                                                           um:precursor_charge_max)
  -spectrum:precursor_charge_min <precursor_charge_min>                    Min charge of precursor charge 
                                                                           range to consider. If specified,
                                                                           also spectrum:override_charge must
                                                                           be set) (default: '1' min: '0')
  -spectrum:precursor_charge_max <precursor_charge_max>                    Max charge of precursor charge 
                                                                           range to consider. If specified,
                                                                           also spectrum:override_charge must
                                                                           be set) (default: '4' min: '0')

Open Search Features:
  -search:track_zero_topn <track_zero_topn>                                Track top N unmodified peptide 
                                                                           results separately from main resul
                                                                           ts internally for boosting feature
                                                                           s. Should be set to a number great
                                                                           er than search:output_report_topN
                                                                           if zero bin boosting is desired
                                                                           (default: '0' min: '0')
  -search:zero_bin_accept_expect <zero_bin_accept_expect>                  Ranks a zero-bin hit above all 
                                                                           non-zero-bin hit if it has expecta
                                                                           tion less than this value (default
                                                                           : '0.0' min: '0.0')
  -search:zero_bin_mult_expect <zero_bin_mult_expect>                      Multiplies expect value of PSMs 
                                                                           in the zero-bin during results
                                                                           ordering (set to less than 1 for
                                                                           boosting) (default: '1.0' min:
                                                                           '0.0')
  -search:add_topn_complementary <add_topn_complementary>                  Inserts complementary ions corresp
                                                                           onding to the top N most intense
                                                                           fragments in each experimental
                                                                           spectrum. Useful for recovery of
                                                                           modified peptides near C-terminus
                                                                           in open search. 0 disables this
                                                                           option (default: '0' min: '0')
  -search:min_fragments_modeling <min_fragments_modeling>                  Minimum number of matched peaks 
                                                                           in PSM for inclusion in statistica
                                                                           l modeling (default: '3' min: '0')
  -search:min_matched_fragments <min_matched_fragments>                    Minimum number of matched peaks 
                                                                           for PSM to be reported. MSFragger
                                                                           recommends a minimum of 4 for narr
                                                                           ow window searching and 6 for open
                                                                           searches (default: '4' min: '0')
  -search:output_report_topn <output_report_topn>                          Reports top N PSMs per input spect
                                                                           rum (default: '1' min: '0')
  -search:output_max_expect <output_max_expect>                            Suppresses reporting of PSM if 
                                                                           top hit has expectation greater
                                                                           than this threshold (default: '50.
                                                                           0' min: '0.0')
  -search:localize_delta_mass <localize_delta_mass>                        Include fragment ions mass-shifted
                                                                           by unknown modifications (recomme
                                                                           nded for open and mass offset sear
                                                                           ches) (0 for OFF, 1 for ON) (defau
                                                                           lt: '0' min: '0')

Static Modification Parameters:
  -statmod:add_cterm_peptide <add_cterm_peptide>                           Statically add mass in Da to C-ter
                                                                           minal of peptide (default: '0.0'
                                                                           min: '0.0')
  -statmod:add_nterm_peptide <add_nterm_peptide>                           Statically add mass in Da to N-ter
                                                                           minal of peptide (default: '0.0'
                                                                           min: '0.0')
  -statmod:add_cterm_protein <add_cterm_protein>                           Statically add mass in Da to C-ter
                                                                           minal of protein (default: '0.0'
                                                                           min: '0.0')
  -statmod:add_nterm_protein <add_nterm_protein>                           Statically add mass in Da to N-ter
                                                                           minal of protein (default: '0.0'
                                                                           min: '0.0')

                                                                           
Common UTIL 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 advan
                                                                           ced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+MSFraggerAdapterPeptide Identification with MSFragger.
Important note:
The Regents of the University of Michigan (âMichiganâ) grants us permission to redistribute
the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available
for use on related service offerings supported by the University of Tubingen and the Center for
Integrative Bioinformatics.
Per the license agreement the use of the pipeline and associated materials is for academic
research, non-commercial or educational purposes. Any commercial use inquiries
must be directed to the University of Michigan Technology Transfer Office at
techtransfer@umich.edu. All right title and interest in MS Fragger shall remain with the
University of Michigan.

For details, please see the supplied license file or
https://raw.githubusercontent.com/OpenMS/THIRDPARTY/master/All/MSFragger/License.txt

version2.7.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'MSFraggerAdapter'

license Set to yes, if you have read and agreed to the MSFragger license terms.yes,no

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_heapmemory3500 Maximum Java heap size (in MB)

executableMSFragger.jar Path to the MSFragger executable to use; may be empty if the executable is globally available.input file

in Input File with specta for MSFraggerinput file*.mzML,*.mzXML

out MSFragger output fileoutput file*.idXML

opt_out MSFragger optional output fileoutput file*.pepXML

database Protein FASTA database file pathinput file*.FASTA,*.fasta,*.fa,*.fas

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

+++toleranceSearch Tolerances

precursor_mass_tolerance_lower20.0 Lower precursor mass tolerance0.0:∞

precursor_mass_tolerance_upper20.0 Upper precursor mass tolerance0.0:∞

precursor_mass_unitppm Unit of precursor mass toleranceDa,ppm

precursor_true_tolerance0.0 True precursor mass tolerance (window is +/- this value). Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches.0.0:∞

precursor_true_unitppm Unit of precursor true toleranceDa,ppm

fragment_mass_tolerance20.0 Fragment mass tolerance (window is +/- this value)0.0:∞

fragment_mass_unitppm Unit of fragment mass toleranceDa,ppm

isotope_error0 Isotope correction for MS/MS events triggered on isotopic peaks. Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12.0,1,2

+++digestIn-Silico Digestion Parameters

search_enzyme_nameTrypsin Name of the enzyme to be written to the pepXML fileArg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Arg-C,Clostripain/P,Trypsin,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage

search_enzyme_cutafterKR Residues after which the enzyme cuts (specified as a string of amino acids)

search_enzyme_nocutbeforeP Residues that the enzyme will not cut before

num_enzyme_terminifully Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)non-enzymatic,semi,fully

allowed_missed_cleavage2 Allowed number of missed cleavages0,1,2,3,4,5

min_length7 Minimum length of peptides to be generated during in-silico digestion0:∞

max_length64 Maximum length of peptides to be generated during in-silico digestion0:∞

mass_range_min500.0 Min mass of peptides to be generated (Da)0.0:∞

mass_range_max5000.0 Max mass of peptides to be generated (Da)0.0:∞

+++varmodVariable Modification Parameters

clip_nterm_mfalse Specifies the trimming of a protein N-terminal methionine as a variable modificationtrue,false

masses[] Masses for variable modifications

syntaxes[] Syntax Strings for variable modifications

enable_commonfalse Enable common variable modifications (15.9949 M and 42.0106 [^)true,false

not_allow_multiple_variable_mods_on_residuefalse Do not allow any one amino acid to be modified by multiple variable modificationstrue,false

max_variable_mods_per_mod2 Maximum number of residues that can be occupied by each variable modification0,1,2,3,4,5

max_variable_mods_combinations5000 Maximum allowed number of modified variably modified peptides from each peptide sequence, (maximum of 65534). If a greater number than the maximum is generated, only the unmodified peptide is considered0:65534

+++spectrumSpectrum Processing Parameters

minimum_peaks10 Minimum number of peaks in experimental spectrum for matching0:∞

use_topn_peaks50 Pre-process experimental spectrum to only use top N peaks0:∞

minimum_ratio0.0 Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity0.0:1.0

clear_mz_range_min0.0 Removes peaks in this m/z range prior to matching (minimum value). Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)0.0:∞

clear_mz_range_max0.0 Removes peaks in this m/z range prior to matching (maximum value). Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)0.0:∞

max_fragment_charge2 Maximum charge state for theoretical fragments to match1,2,3,4

override_chargefalse Ignores precursor charge and uses charge state specified in precursor_charge range (parameters: spectrum:precursor_charge_min and spectrum:precursor_charge_max)true,false

precursor_charge_min1 Min charge of precursor charge range to consider. If specified, also spectrum:override_charge must be set)0:∞

precursor_charge_max4 Max charge of precursor charge range to consider. If specified, also spectrum:override_charge must be set)0:∞

+++searchOpen Search Features

track_zero_topn0 Track top N unmodified peptide results separately from main results internally for boosting features. Should be set to a number greater than search:output_report_topN if zero bin boosting is desired0:∞

zero_bin_accept_expect0.0 Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value0.0:∞

zero_bin_mult_expect1.0 Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting)0.0:∞

add_topn_complementary0 Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectrum. Useful for recovery of modified peptides near C-terminus in open search. 0 disables this option0:∞

min_fragments_modeling3 Minimum number of matched peaks in PSM for inclusion in statistical modeling0:∞

min_matched_fragments4 Minimum number of matched peaks for PSM to be reported. MSFragger recommends a minimum of 4 for narrow window searching and 6 for open searches0:∞

output_report_topn1 Reports top N PSMs per input spectrum0:∞

output_max_expect50.0 Suppresses reporting of PSM if top hit has expectation greater than this threshold0.0:∞

localize_delta_mass0 Include fragment ions mass-shifted by unknown modifications (recommended for open and mass offset searches) (0 for OFF, 1 for ON)0:∞

+++statmodStatic Modification Parameters

add_cterm_peptide0.0 Statically add mass in Da to C-terminal of peptide0.0:∞

add_nterm_peptide0.0 Statically add mass in Da to N-terminal of peptide0.0:∞

add_cterm_protein0.0 Statically add mass in Da to C-terminal of protein0.0:∞

add_nterm_protein0.0 Statically add mass in Da to N-terminal of protein0.0:∞

add_G_glycine0.0 Statically add mass to glycine0.0:∞

add_A_alanine0.0 Statically add mass to alanine0.0:∞

add_S_serine0.0 Statically add mass to serine0.0:∞

add_P_proline0.0 Statically add mass to proline0.0:∞

add_V_valine0.0 Statically add mass to valine0.0:∞

add_T_threonine0.0 Statically add mass to threonine0.0:∞

add_C_cysteine57.021464000000002 Statically add mass to cysteine0.0:∞

add_L_leucine0.0 Statically add mass to leucine0.0:∞

add_I_isoleucine0.0 Statically add mass to isoleucine0.0:∞

add_N_asparagine0.0 Statically add mass to asparagine0.0:∞

add_D_aspartic_acid0.0 Statically add mass to aspartic_acid0.0:∞

add_Q_glutamine0.0 Statically add mass to glutamine0.0:∞

add_K_lysine0.0 Statically add mass to lysine0.0:∞

add_E_glutamic_acid0.0 Statically add mass to glutamic_acid0.0:∞

add_M_methionine0.0 Statically add mass to methionine0.0:∞

add_H_histidine0.0 Statically add mass to histidine0.0:∞

add_F_phenylalanine0.0 Statically add mass to phenylalanine0.0:∞

add_R_arginine0.0 Statically add mass to arginine0.0:∞

add_Y_tyrosine0.0 Statically add mass to tyrosine0.0:∞

add_W_tryptophan0.0 Statically add mass to tryptophan0.0:∞