IDFilter

Options

version

Version of the tool that generated this parameters file.

var_mods

Keep only peptide hits with variable modifications (as defined in the 'SearchParameters' section of the input file).

remove_duplicate_psm

Removes duplicated PSMs per spectrum and retains the one with the higher score.

remove_shared_peptides

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:protein' or 'thresh:prot'.

remove_peptide_hits_by_metavalue

Expects a 3-tuple (=3 entries in the list), i.e. <name> 'lt|eq|gt|ne' <value>; the first is the name of meta value, followed by the comparison operator (equal, less, greater, not equal) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!

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)

rt

Retention time range to extract.

mz

Mass-to-charge range to extract.

length

Keep only peptide hits with a sequence length in this range.

charge

Keep only peptide hits with charge states in this range.

psm

The score which should be reached by a peptide hit to be kept. (use 'NAN' to disable this filter)

peptide

The score which should be reached by a peptide hit to be kept. (use 'NAN' to disable this filter)

type_peptide

Score used for filtering. If empty, the main score is used.

protein

The score which should be reached by a protein hit to be kept. All proteins are filtered based on their singleton scores irrespective of grouping. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides. (use 'NAN' to disable this filter)

type_protein

The type of the score which should be reached by a protein hit to be kept. If empty, the most recently set score is used.

proteingroup

The score which should be reached by a protein group to be kept. Performs group level score filtering (including groups of single proteins). Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides. (use 'NAN' to disable this filter)

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)

RegEx

Remove all peptides with (unmodified) sequences matched by the RegEx e.g. [BJXZ] removes ambiguous peptides.

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_spectra

Keep only the 'n' best spectra (i.e., PeptideIdentifications) (for n > 0). A spectrum is considered better if it has a higher scoring peptide hit than the other spectrum.

n_peptide_hits

Keep only the 'n' highest scoring peptide hits per spectrum (for n > 0).

spectrum_per_peptide

Keep one spectrum per peptide. Value determines if same sequence but different charges or modifications are treated as separate peptides or the same peptide. (default: false = filter disabled).

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

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.)

Workflows

• 01-MaCProQCKNIME Hub
• 02-download_and_analyze_raw_fileKNIME Hub
• 02-PIA_and_quantKNIME Hub
• FDR FilteringKNIME Hub
• Identification_quantification_with_inference_isobaric_epifany_MSstatsTMTOpenMS
• Show all 13 workflows

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