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IDFilter

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261316 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Filters results from protein or peptide identification engines based on different criteria.

Web Documentation for IDFilter

Options

version
Version of the tool that generated this parameters file.
length
Keep only peptide hits with a sequence length in this range.
charge
Keep only peptide hits with charge states in this range.
var_mods
Keep only peptide hits with variable modifications (as defined in the 'SearchParameters' section of the input file).
unique
If a peptide hit occurs more than once per peptide ID, only one instance is kept.
unique_per_protein
Only peptides matching exactly one protein are kept. Remember that isoforms count as different proteins!
keep_unreferenced_protein_hits
Proteins not referenced by a peptide are retained in the IDs.
remove_decoys
Remove proteins according to the information in the user parameters. Usually used in combination with 'delete_unreferenced_peptide_hits'.
delete_unreferenced_peptide_hits
Peptides not referenced by any protein are deleted in the IDs. Usually used in combination with 'score:prot' or 'thresh:prot'.
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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
rt
Retention time range to extract.
mz
Mass-to-charge range to extract.
pep
The score which should be reached by a peptide hit to be kept.
prot
The score which should be reached by a protein hit to be kept. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides.
pep
Keep a peptide hit only if its score is above this fraction of the peptide significance threshold.
prot
Keep a protein hit only if its score is above this fraction of the protein significance threshold. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides.
protein_accessions
All peptides that do not reference at least one of the provided protein accession are removed. Only proteins of the provided list are retained.
ignore_modifications
Compare whitelisted peptides by sequence only.
modifications
Keep only peptides with sequences that contain (any of) the selected modification(s)
protein_accessions
All peptides that reference at least one of the provided protein accession are removed. Only proteins not in the provided list are retained.
ignore_modifications
Compare blacklisted peptides by sequence only.
modifications
Remove all peptides with sequences that contain (any of) the selected modification(s)
enzyme
enzyme used for the digestion of the sample
specificity
Specificity of the filter
missed_cleavages
range of allowed missed cleavages in the peptide sequences By default missed cleavages are ignored
methionine_cleavage
Allow methionine cleavage at the N-terminus of the protein.
number_of_missed_cleavages
range of allowed missed cleavages in the peptide sequences. For example: 0:1 -> peptides with two or more missed cleavages will be removed, 0:0 -> peptides with any missed cleavages will be removed
enzyme
enzyme used for the digestion of the sample
p_value
Retention time filtering by the p-value predicted by RTPredict.
p_value_1st_dim
Retention time filtering by the p-value predicted by RTPredict for first dimension.
error
Filtering by deviation to theoretical mass (disabled for negative values).
unit
Absolute or relative error.
n_peptide_hits
Keep only the 'n' highest scoring peptide hits per spectrum (for n > 0).
n_protein_hits
Keep only the 'n' highest scoring protein hits (for n > 0).
strict
Keep only the highest scoring peptide hit. Similar to n_peptide_hits=1, but if there are ties between two or more highest scoring hits, none are kept.
n_to_m_peptide_hits
Peptide hit rank range to extracts

Input Ports

input file [idXML]
Filename of a FASTA file containing protein sequences.#br#All peptides that are not referencing a protein in this file are removed.#br#All proteins whose accessions are not present in this file are removed. [fasta,opt.]
Only peptides with the same sequence and modification assignment as any peptide in this file are kept. Use with 'whitelist:ignore_modifications' to only compare by sequence.#br# [idXML,opt.]
Filename of a FASTA file containing protein sequences.#br#All peptides that are referencing a protein in this file are removed.#br#All proteins whose accessions are present in this file are removed. [fasta,opt.]
Peptides with the same sequence and modification assignment as any peptide in this file are filtered out. Use with 'blacklist:ignore_modifications' to only compare by sequence.#br# [idXML,opt.]
fasta protein sequence database. [fasta,opt.]

Output Ports

output file [idXML]

Views

IDFilter Std Output
The text sent to standard out during the execution of IDFilter.
IDFilter Error Output
The text sent to standard error during the execution of IDFilter. (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 4.0
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