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MSFraggerAdapter

Generic Workflow Nodes for KNIME: OpenMS version 2.6.0.202009301213 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Peptide Identification with MSFragger

Web Documentation for MSFraggerAdapter

Options

version
Version of the tool that generated this parameters file.
java_heapmemory
Maximum Java heap size (in MB)
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
precursor_mass_tolerance
Precursor mass tolerance (window is +/- this value)
precursor_mass_unit
Unit of precursor mass tolerance
precursor_true_tolerance
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.
precursor_true_unit
Unit of precursor true tolerance
fragment_mass_tolerance
Fragment mass tolerance (window is +/- this value)
fragment_mass_unit
Unit of fragment mass tolerance
isotope_error
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.
search_enzyme_name
Name of the enzyme to be written to the pepXML file
search_enzyme_cutafter
Residues after which the enzyme cuts (specified as a string of amino acids)
search_enzyme_nocutbefore
Residues that the enzyme will not cut before
num_enzyme_termini
Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)
allowed_missed_cleavage
Allowed number of missed cleavages
min_length
Minimum length of peptides to be generated during in-silico digestion
max_length
Maximum length of peptides to be generated during in-silico digestion
mass_range_min
Min mass of peptides to be generated (Da)
mass_range_max
Max mass of peptides to be generated (Da)
clip_nterm_m
Specifies the trimming of a protein N-terminal methionine as a variable modification
masses
Masses for variable modifications
syntaxes
Syntax Strings for variable modifications
enable_common
Enable common variable modifications (15.9949 M and 42.0106 [^)
not_allow_multiple_variable_mods_on_residue
Do not allow any one amino acid to be modified by multiple variable modifications
max_variable_mods_per_mod
Maximum number of residues that can be occupied by each variable modification
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
minimum_peaks
Minimum number of peaks in experimental spectrum for matching
use_topn_peaks
Pre-process experimental spectrum to only use top N peaks
minimum_ratio
Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity
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)
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)
max_fragment_charge
Maximum charge state for theoretical fragments to match
override_charge
Ignores precursor charge and uses charge state specified in precursor_charge range (parameters: spectrum:precursor_charge_min and spectrum:precursor_charge_max)
precursor_charge_min
Min charge of precursor charge range to consider. If specified, also spectrum:override_charge must be set)
precursor_charge_max
Max charge of precursor charge range to consider. If specified, also spectrum:override_charge must be set)
track_zero_topn
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 desired
zero_bin_accept_expect
Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value
zero_bin_mult_expect
Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting)
add_topn_complementary
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 option
min_fragments_modeling
Minimum number of matched peaks in PSM for inclusion in statistical modeling
min_matched_fragments
Minimum number of matched peaks for PSM to be reported. MSFragger recommends a minimum of 4 for narrow window searching and 6 for open searches
output_report_topn
Reports top N PSMs per input spectrum
output_max_expect
Suppresses reporting of PSM if top hit has expectation greater than this threshold
add_cterm_peptide
Statically add mass in Da to C-terminal of peptide
add_nterm_peptide
Statically add mass in Da to N-terminal of peptide
add_cterm_protein
Statically add mass in Da to C-terminal of protein
add_nterm_protein
Statically add mass in Da to N-terminal of protein
add_G_glycine
Statically add mass to glycine
add_A_alanine
Statically add mass to alanine
add_S_serine
Statically add mass to serine
add_P_proline
Statically add mass to proline
add_V_valine
Statically add mass to valine
add_T_threonine
Statically add mass to threonine
add_C_cysteine
Statically add mass to cysteine
add_L_leucine
Statically add mass to leucine
add_I_isoleucine
Statically add mass to isoleucine
add_N_asparagine
Statically add mass to asparagine
add_D_aspartic_acid
Statically add mass to aspartic_acid
add_Q_glutamine
Statically add mass to glutamine
add_K_lysine
Statically add mass to lysine
add_E_glutamic_acid
Statically add mass to glutamic_acid
add_M_methionine
Statically add mass to methionine
add_H_histidine
Statically add mass to histidine
add_F_phenylalanine
Statically add mass to phenylalanine
add_R_arginine
Statically add mass to arginine
add_Y_tyrosine
Statically add mass to tyrosine
add_W_tryptophan
Statically add mass to tryptophan

Input Ports

Icon
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 [,opt.]
Icon
Path to the MSFragger executable to use; may be empty if the executable is globally available. [,opt.]
Icon
Input File with specta for MSFragger [mzML,mzXML]
Icon
Protein FASTA database file path [FASTA,fasta,fa,fas]

Output Ports

Icon
MSFragger output file [idXML]
Icon
MSFragger optional output file [pepXML]

Views

MSFraggerAdapter Std Output
The text sent to standard out during the execution of MSFraggerAdapter.
MSFraggerAdapter Error Output
The text sent to standard error during the execution of MSFraggerAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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