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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

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

Web Documentation for MSFraggerAdapter

Options

version: Version of the tool that generated this parameters file.
license: Set to yes, if you have read and agreed to the MSFragger license terms.
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_lower: Lower precursor mass tolerance
precursor_mass_tolerance_upper: Upper precursor mass tolerance
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
localize_delta_mass: Include fragment ions mass-shifted by unknown modifications (recommended for open and mass offset searches) (0 for OFF, 1 for ON)
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

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

Output Ports

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

Popular Predecessors

Popular Successors

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.)

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Installation

To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v4.7

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Plugin version: 2.7.0.202109131426

On NodePit since: 2022-12-06

Last update: 2024-04-13

KNIME versions: From v3.6 to v4.7

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