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MSGFPlusAdapter

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

MS/MS database search using MS-GF+.

Web Documentation for MSGFPlusAdapter

Options

version
Version of the tool that generated this parameters file.
add_decoys
Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda'). This allows the calculation of FDRs, but should only be used if the database does not already contain decoys.
precursor_mass_tolerance
Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')
precursor_error_units
Unit of precursor mass tolerance (MS-GF+ parameter '-t')
isotope_error_range
Range of allowed isotope peak errors (MS-GF+ parameter '-ti'). Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| < 20 ppm' for n = -1, 0, 1, 2.
fragment_method
Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m')
instrument
Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst')
enzyme
Enzyme used for digestion, or type of cleavage. Note: MS-GF+ does not support blocking rules. (MS-GF+ parameter '-e')
protocol
Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')
tryptic
Level of cleavage specificity required (MS-GF+ parameter '-ntt')
min_precursor_charge
Minimum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-minCharge')
max_precursor_charge
Maximum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-maxCharge')
min_peptide_length
Minimum peptide length to consider (MS-GF+ parameter '-minLength')
max_peptide_length
Maximum peptide length to consider (MS-GF+ parameter '-maxLength')
matches_per_spec
Number of matches per spectrum to be reported (MS-GF+ parameter '-n')
add_features
Output additional features (MS-GF+ parameter '-addFeatures'). This is required by Percolator and hence by default enabled.
max_mods
Maximum number of modifications per peptide. If this value is large, the search may take very long.
max_missed_cleavages
Maximum number of missed cleavages allowed for a peptide to be considered for scoring. (default: -1 meaning unlimited)
tasks
(Override the number of tasks to use on the threads; Default: (internally calculated based on inputs)) More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs). 1 <= tasks <= numThreads: will create one task per thread, which is the original behavior. tasks = 0: use default calculation - minimum of: (threads*3) and (numSpectra/250). tasks < 0: multiply number of threads by abs(tasks) to determine number of tasks (i.e., -2 means "2 * numThreads" tasks). One task per thread will use the most memory, but will usually finish the fastest. 2-3 tasks per thread will use comparably less memory, but may cause the search to take 1.5 to 2 times as long.
fixed_modifications
Fixed modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
variable_modifications
Variable modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
legacy_conversion
Use the indirect conversion of MS-GF+ results to idXML via export to TSV. Try this only if the default conversion takes too long or uses too much memory.
java_memory
Maximum Java heap size (in MB)
java_permgen
Maximum Java permanent generation space (in MB); only for Java 7 and below
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)

Input Ports

Icon
Input file (MS-GF+ parameter '-s') [mzML,mzXML,mgf,ms2]
Icon
Protein sequence database (FASTA file; MS-GF+ parameter '-d'). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'. [FASTA]
Icon
Optional MSGF+ configuration file (passed as -conf <file> to MSGF+). See documentation for examples. Parameters of the adapter take precedence. Use conf file only for settings not available here (for example, any fixed/var modifications, in the conf file will be ignored, since they are provided via -mod flag) [,opt.]
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.]

Output Ports

Icon
Output file [idXML]
Icon
Alternative output file (MS-GF+ parameter '-o')#br#Either 'out' or 'mzid_out' are required. They can be used together. [mzid]

Views

MSGFPlusAdapter Std Output
The text sent to standard out during the execution of MSGFPlusAdapter.
MSGFPlusAdapter Error Output
The text sent to standard error during the execution of MSGFPlusAdapter. (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)

Workflows

Installation

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

KNIME 4.2

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

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Developers

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