FileFilter

Extracts portions of the data from an mzML, featureXML or consensusXML file.

pot. predecessor tools	→ FileFilter →	pot. successor tools
any tool yielding output in mzML, featureXML or consensusXML format		any tool that profits on reduced input

With this tool it is possible to extract m/z, retention time and intensity ranges from an input file and to write all data that lies within the given ranges to an output file.

Depending on the input file type, additional specific operations are possible:

• mzML
  • extract spectra of a certain MS level
  • filter by signal-to-noise estimation
  • filter by scan mode of the spectra
  • filter by scan polarity of the spectra
• remove MS2 scans whose precursor matches identifications (from an idXML file in 'id:blacklist')
• featureXML
  • filter by feature charge
  • filter by feature size (number of subordinate features)
  • filter by overall feature quality
• consensusXML
  • filter by size (number of elements in consensus features)
  • filter by consensus feature charge
  • filter by map (extracts specified maps and re-evaluates consensus centroid)
    e.g. FileFilter -map 2 3 5 -in file1.consensusXML -out file2.consensusXML
    If a single map is specified, the feature itself can be extracted.
    e.g. FileFilter -map 5 -in file1.consensusXML -out file2.featureXML
• featureXML / consensusXML:
• remove items with a certain meta value annotation. Allowing for >, < and = comparisons. List types are compared by length, not content. Integer, Double and String are compared using their build-in operators.
  • filter sequences, e.g. "LYSNLVER" or the modification "(Phospho)"
    e.g. FileFilter -id:sequences_whitelist Phospho -in file1.consensusXML -out file2.consensusXML
  • filter accessions, e.g. "sp|P02662|CASA1_BOVIN"
  • remove features with annotations
  • remove features without annotations
  • remove unassigned peptide identifications
  • filter id with best score of features with multiple peptide identifications
    e.g. FileFilter -id:remove_unannotated_features -id:remove_unassigned_ids -id:keep_best_score_id -in file1.featureXML -out file2.featureXML
  • remove features with id clashes (different sequences mapped to one feature)

The priority of the id-flags is (decreasing order): remove_annotated_features / remove_unannotated_features -> remove_clashes -> keep_best_score_id -> sequences_whitelist / accessions_whitelist

MS2 and higher spectra can be filtered according to precursor m/z (see 'peak_options:pc_mz_range'). This flag can be combined with 'rt' range to filter precursors by RT and m/z. If you want to extract an MS1 region with untouched MS2 spectra included, you will need to split the dataset by MS level, then use the 'mz' option for MS1 data and 'peak_options:pc_mz_range' for MS2 data. Afterwards merge the two files again. RT can be filtered at any step.

Note

For filtering peptide/protein identification data, see the IDFilter tool.

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

FileFilter -- Extracts or manipulates portions of data from peak, feature or consensus-feature files.
Full documentation: http://www.openms.de/doxygen/release/3.1.0/html/TOPP_FileFilter.html
Version: 3.1.0 Oct 18 2023, 10:27:18, Revision: 17a07f8
To cite OpenMS:
 + Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for 
   mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  FileFilter <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option

Options (mandatory options marked with '*'):
  -in <file>*                                                  Input file (valid formats: 'mzML', 'featureXML
                                                               ', 'consensusXML')
  -in_type <type>                                              Input file type -- default: determined from 
                                                               file extension or content (valid: 'mzML', 'fea
                                                               tureXML', 'consensusXML')
  -out <file>*                                                 Output file (valid formats: 'mzML', 'featureXM
                                                               L', 'consensusXML')
  -out_type <type>                                             Output file type -- default: determined from 
                                                               file extension or content (valid: 'mzML', 'fea
                                                               tureXML', 'consensusXML')
  -rt [min]:[max]                                              Retention time range to extract (default: ':')

  -mz [min]:[max]                                              M/z range to extract (applies to ALL ms levels
                                                               !) (default: ':')
  -int [min]:[max]                                             Intensity range to extract (default: ':')
  -sort                                                        Sorts the output according to RT and m/z.

Peak data options:
  -peak_options:sn <s/n ratio>                                 Write peaks with S/N > 'sn' values only (defau
                                                               lt: '0.0')
  -peak_options:rm_pc_charge i j ...                           Remove MS(2) spectra with these precursor char
                                                               ges. All spectra without precursor are kept!
  -peak_options:pc_mz_range [min]:[max]                        MSn (n>=2) precursor filtering according to 
                                                               their m/z value. Do not use this flag in conju
                                                               nction with 'mz', unless you want to actually 
                                                               remove peaks in spectra (see 'mz'). RT filteri
                                                               ng is covered by 'rt' and compatible with this
                                                                flag. (default: ':')
  -peak_options:pc_mz_list mz_1 mz_2 ...                       List of m/z values. If a precursor window cove
                                                               rs ANY of these values, the corresponding MS/M
                                                               S spectrum will be kept.
  -peak_options:level i j ...                                  MS levels to extract (default: '[1 2 3]')
  -peak_options:sort_peaks                                     Sorts the peaks according to m/z
  -peak_options:no_chromatograms                               No conversion to space-saving real chromatogra
                                                               ms, e.g. from SRM scans
  -peak_options:remove_chromatograms                           Removes chromatograms stored in a file
  -peak_options:remove_empty                                   Removes spectra and chromatograms without peak
                                                               s.
  -peak_options:mz_precision 32 or 64                          Store base64 encoded m/z data using 32 or 64 
                                                               bit precision (default: '64') (valid: '32', 
                                                               '64')
  -peak_options:int_precision 32 or 64                         Store base64 encoded intensity data using 32 
                                                               or 64 bit precision (default: '32') (valid: 
                                                               '32', '64')
  -peak_options:indexed_file true or false                     Whether to add an index to the file when writi
                                                               ng (default: 'true') (valid: 'true', 'false')
  -peak_options:zlib_compression true or false                 Whether to store data with zlib compression 
                                                               (lossless compression) (default: 'false') (val
                                                               id: 'true', 'false')

Numpress compression for peak data:
  -peak_options:numpress:masstime <compression_scheme>         Apply MS Numpress compression algorithms in 
                                                               m/z or rt dimension (recommended: linear) (def
                                                               ault: 'none') (valid: 'none', 'linear', 'pic',
                                                                'slof')
  -peak_options:numpress:intensity <compression_scheme>        Apply MS Numpress compression algorithms in 
                                                               intensity dimension (recommended: slof or pic)
                                                                (default: 'none') (valid: 'none', 'linear', 
                                                               'pic', 'slof')
  -peak_options:numpress:float_da <compression_scheme>         Apply MS Numpress compression algorithms for 
                                                               the float data arrays (recommended: slof or 
                                                               pic) (default: 'none') (valid: 'none', 'linear
                                                               ', 'pic', 'slof')

Remove spectra or select spectra (removing all others) with certain properties:
  -spectra:remove_zoom                                         Remove zoom (enhanced resolution) scans
  -spectra:remove_mode <mode>                                  Remove scans by scan mode (valid: 'Unknown', 
                                                               'MassSpectrum', 'MS1Spectrum', 'MSnSpectrum', 
                                                               'SelectedIonMonitoring', 'SelectedReactionMoni
                                                               toring', 'ConsecutiveReactionMonitoring', 'Con
                                                               stantNeutralGain', 'ConstantNeutralLoss', 'Pre
                                                               cursor', 'EnhancedMultiplyCharged', 'TimeDelay
                                                               edFragmentation', 'ElectromagneticRadiation', 
                                                               'Emission', 'Absorption')

                                                               

Remove spectra or select spectra (removing all others) with certain properties:
  -spectra:remove_activation <activation>                      Remove MSn scans where any of its precursors 
                                                               features a certain activation method (valid: 
                                                               'Collision-induced dissociation', 'Post-source
                                                                decay', 'Plasma desorption', 'Surface-induced
                                                                dissociation', 'Blackbody infrared radiative 
                                                               dissociation', 'Electron capture dissociation'
                                                               , 'Infrared multiphoton dissociation', 'Sustai
                                                               ned off-resonance irradiation', 'High-energy 
                                                               collision-induced dissociation', 'Low-energy 
                                                               ...
                                                               dissociation', 'Bruker proprietary method')
  -spectra:remove_collision_energy [min]:[max]                 Remove MSn scans with a collision energy in 
                                                               the given interval (default: ':')
  -spectra:remove_isolation_window_width [min]:[max]           Remove MSn scans whose isolation window width 
                                                               is in the given interval (default: ':')

                                                               

Remove spectra or select spectra (removing all others) with certain properties:
  -spectra:select_zoom                                         Select zoom (enhanced resolution) scans
  -spectra:select_mode <mode>                                  Selects scans by scan mode
                                                                (valid: 'Unknown', 'MassSpectrum', 'MS1Spectr
                                                               um', 'MSnSpectrum', 'SelectedIonMonitoring', 
                                                               'SelectedReactionMonitoring', 'ConsecutiveReac
                                                               tionMonitoring', 'ConstantNeutralGain', 'Const
                                                               antNeutralLoss', 'Precursor', 'EnhancedMultipl
                                                               yCharged', 'TimeDelayedFragmentation', 'Electr
                                                               omagneticRadiation', 'Emission', 'Absorption')

  -spectra:select_activation <activation>                      Retain MSn scans where any of its precursors 
                                                               features a certain activation method (valid: 
                                                               'Collision-induced dissociation', 'Post-source
                                                                decay', 'Plasma desorption', 'Surface-induced
                                                                dissociation', 'Blackbody infrared radiative 
                                                               dissociation', 'Electron capture dissociation'
                                                               , 'Infrared multiphoton dissociation', 'Sustai
                                                               ned off-resonance irradiation', 'High-energy 
                                                               collision-induced dissociation', 'Low-energy 
                                                               ...
                                                               dissociation', 'Bruker proprietary method')
  -spectra:select_collision_energy [min]:[max]                 Select MSn scans with a collision energy in 
                                                               the given interval (default: ':')
  -spectra:select_isolation_window_width [min]:[max]           Select MSn scans whose isolation window width 
                                                               is in the given interval (default: ':')

                                                               

Remove spectra or select spectra (removing all others) with certain properties:
  -spectra:select_polarity <polarity>                          Retain MSn scans with a certain scan polarity 
                                                               (valid: 'unknown', 'positive', 'negative')

Black or white listing of of MS2 spectra by spectral similarity:
  -spectra:blackorwhitelist:file <file>                        Input file containing MS2 spectra that should 
                                                               be retained or removed from the mzML file!
                                                               Matching tolerances are taken from 'spectra:bl
                                                               ackorwhitelist:similarity_threshold|rt|mz' 
                                                               options.
                                                                (valid formats: 'mzML')
  -spectra:blackorwhitelist:similarity_threshold <similarity>  Similarity threshold when matching MS2 spectra
                                                               . (-1 = disabled). (default: '-1.0') (min: 
                                                               '-1.0' max: '1.0')
  -spectra:blackorwhitelist:rt tolerance                       Retention tolerance [s] when matching precurso
                                                               r positions. (-1 = disabled) (default: '0.01')

  -spectra:blackorwhitelist:mz tolerance                       M/z tolerance [Th] when matching precursor 
                                                               positions. (-1 = disabled) (default: '0.01')
  -spectra:blackorwhitelist:use_ppm_tolerance                  If ppm tolerance should be used. Otherwise Da 
                                                               are used. (default: 'false')
  -spectra:blackorwhitelist:blacklist                          True: remove matched MS2. False: retain matche
                                                               d MS2 spectra. Other levels are kept (default:
                                                                'true') (valid: 'false', 'true')

Remove spectra or select spectra (removing all others) with certain properties:
  -spectra:replace_pc_charge in_charge:out_charge              Replaces in_charge with out_charge in all prec
                                                               ursors. (default: ':')

                                                               

Feature data options:
  -feature:q [min]:[max]                                       Overall quality range to extract [0:1] (defaul
                                                               t: ':')

                                                               

Consensus feature data options:
  -consensus:map i j ...                                       Non-empty list of maps to be extracted from a 
                                                               consensus (indices are 0-based).
  -consensus:map_and                                           Consensus features are kept only if they conta
                                                               in exactly one feature from each map (as given
                                                                above in 'map')

Black or white listing of of MS2 spectra by consensus features:
  -consensus:blackorwhitelist:blacklist                        True: remove matched MS2. False: retain matche
                                                               d MS2 spectra. Other levels are kept (default:
                                                                'true') (valid: 'false', 'true')
  -consensus:blackorwhitelist:file <file>                      Input file containing consensus features whose
                                                                corresponding MS2 spectra should be removed 
                                                               from the mzML file!
                                                               Matching tolerances are taken from 'consensus:
                                                               blackorwhitelist:rt' and 'consensus:blackorwhi
                                                               telist:mz' options.
                                                               If consensus:blackorwhitelist:maps is specifie
                                                               d, only these will be used.
                                                                (valid formats: 'consensusXML')
  -consensus:blackorwhitelist:maps i j ...                     Maps used for black/white list filtering
  -consensus:blackorwhitelist:rt tolerance                     Retention tolerance [s] for precursor to conse
                                                               nsus feature position (default: '60.0') (min: 
                                                               '0.0')
  -consensus:blackorwhitelist:mz tolerance                     M/z tolerance [Th] for precursor to consensus 
                                                               feature position (default: '0.01') (min: '0.0'
                                                               )
  -consensus:blackorwhitelist:use_ppm_tolerance                If ppm tolerance should be used. Otherwise Da 
                                                               are used. (default: 'false') (valid: 'false', 
                                                               'true')

                                                               

Feature & Consensus data options:
  -f_and_c:charge [min]:[max]                                  Charge range to extract (default: ':')
  -f_and_c:size [min]:[max]                                    Size range to extract (default: ':')
  -f_and_c:remove_meta <name> 'lt|eq|gt' <value>               Expects a 3-tuple (=3 entries in the list), 
                                                               i.e. <name> 'lt|eq|gt' <value>; the first is 
                                                               the name of meta value, followed by the compar
                                                               ison operator (equal, less or greater) and 
                                                               the value to compare to. All comparisons are 
                                                               done after converting the given value to the 
                                                               corresponding data value type of the meta valu
                                                               e (for lists, this simply compares length, 
                                                               not content!)!
  -f_and_c:remove_hull                                         Remove hull from features.

                                                               

ID options. The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -> remov
e_clashes -> keep_best_score_id -> sequences_whitelist  / accessions_whitelist:
  -id:keep_best_score_id                                       In case of multiple peptide identifications, 
                                                               keep only the id with best score
  -id:sequences_whitelist <sequence>                           Keep only features containing whitelisted subs
                                                               trings, e.g. features containing LYSNLVER or 
                                                               the modification (Oxidation). To control compa
                                                               rison method used for whitelisting, see 'id:se
                                                               quence_comparison_method'.
  -id:accessions_whitelist <accessions>                        Keep only features with white listed accession
                                                               s, e.g. sp|P02662|CASA1_BOVIN
  -id:remove_annotated_features                                Remove features with annotations
  -id:remove_unannotated_features                              Remove features without annotations
  -id:remove_unassigned_ids                                    Remove unassigned peptide identifications
  -id:blacklist <file>                                         Input file containing MS2 identifications whos
                                                               e corresponding MS2 spectra should be removed 
                                                               from the mzML file!
                                                               Matching tolerances are taken from 'id:rt' 
                                                               and 'id:mz' options.
                                                               This tool will require all IDs to be matched 
                                                               to an MS2 spectrum, and quit with error otherw
                                                               ise. Use 'id:blacklist_imperfect' to allow 
                                                               for mismatches. (valid formats: 'idXML')
  -id:rt tolerance                                             Retention tolerance [s] for precursor to id 
                                                               position (default: '0.1') (min: '0.0')
  -id:mz tolerance                                             M/z tolerance [Th] for precursor to id positio
                                                               n (default: '1.0e-03') (min: '0.0')
  -id:blacklist_imperfect                                      Allow for mismatching precursor positions (see
                                                                'id:blacklist')

                                                               
                                                               
Common TOPP options:
  -ini <file>                                                  Use the given TOPP INI file
  -threads <n>                                                 Sets the number of threads allowed to be used 
                                                               by the TOPP tool (default: '1')
  -write_ini <file>                                            Writes the default configuration file
  --help                                                       Shows options
  --helphelp                                                   Shows all options (including advanced)

The following configuration subsections are valid:
 - algorithm   S/N algorithm section

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
For more information, please consult the online documentation for this tool:
  - http://www.openms.de/doxygen/release/3.1.0/html/TOPP_FileFilter.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+FileFilterExtracts or manipulates portions of data from peak, feature or consensus-feature files.

version3.1.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'FileFilter'

in Input fileinput file*.mzML, *.featureXML, *.consensusXML

in_type Input file type -- default: determined from file extension or contentmzML, featureXML, consensusXML

out Output fileoutput file*.mzML, *.featureXML, *.consensusXML

out_type Output file type -- default: determined from file extension or contentmzML, featureXML, consensusXML

rt: Retention time range to extract

mz: m/z range to extract (applies to ALL ms levels!)

int: Intensity range to extract

sortfalse Sorts the output according to RT and m/z.true, false

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false

+++peak_optionsPeak data options

sn0.0 Write peaks with S/N > 'sn' values only

rm_pc_charge[] Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!

pc_mz_range: MSn (n>=2) precursor filtering according to their m/z value. Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag.

pc_mz_list[] List of m/z values. If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept.

level[1, 2, 3] MS levels to extract

sort_peaksfalse Sorts the peaks according to m/ztrue, false

no_chromatogramsfalse No conversion to space-saving real chromatograms, e.g. from SRM scanstrue, false

remove_chromatogramsfalse Removes chromatograms stored in a filetrue, false

remove_emptyfalse Removes spectra and chromatograms without peaks.true, false

mz_precision64 Store base64 encoded m/z data using 32 or 64 bit precision32, 64

int_precision32 Store base64 encoded intensity data using 32 or 64 bit precision32, 64

indexed_filetrue Whether to add an index to the file when writingtrue, false

zlib_compressionfalse Whether to store data with zlib compression (lossless compression)true, false

++++numpressNumpress compression for peak data

masstimenone Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)none, linear, pic, slof

lossy_mass_accuracy-1.0 Desired (absolute) m/z accuracy for lossy compression (e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy).

intensitynone Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)none, linear, pic, slof

float_danone Apply MS Numpress compression algorithms for the float data arrays (recommended: slof or pic)none, linear, pic, slof

+++spectraRemove spectra or select spectra (removing all others) with certain properties

remove_zoomfalse Remove zoom (enhanced resolution) scanstrue, false

remove_mode Remove scans by scan modeUnknown, MassSpectrum, MS1Spectrum, MSnSpectrum, SelectedIonMonitoring, SelectedReactionMonitoring, ConsecutiveReactionMonitoring, ConstantNeutralGain, ConstantNeutralLoss, Precursor, EnhancedMultiplyCharged, TimeDelayedFragmentation, ElectromagneticRadiation, Emission, Absorption

remove_activation Remove MSn scans where any of its precursors features a certain activation methodCollision-induced dissociation, Post-source decay, Plasma desorption, Surface-induced dissociation, Blackbody infrared radiative dissociation, Electron capture dissociation, Infrared multiphoton dissociation, Sustained off-resonance irradiation, High-energy collision-induced dissociation, Low-energy collision-induced dissociation, Photodissociation, Electron transfer dissociation, Pulsed q dissociation, trap-type collision-induced dissociation, beam-type collision-induced dissociation, in-source collision-induced dissociation, Bruker proprietary method

remove_collision_energy: Remove MSn scans with a collision energy in the given interval

remove_isolation_window_width: Remove MSn scans whose isolation window width is in the given interval

select_zoomfalse Select zoom (enhanced resolution) scanstrue, false

select_mode Selects scans by scan mode
Unknown, MassSpectrum, MS1Spectrum, MSnSpectrum, SelectedIonMonitoring, SelectedReactionMonitoring, ConsecutiveReactionMonitoring, ConstantNeutralGain, ConstantNeutralLoss, Precursor, EnhancedMultiplyCharged, TimeDelayedFragmentation, ElectromagneticRadiation, Emission, Absorption

select_activation Retain MSn scans where any of its precursors features a certain activation methodCollision-induced dissociation, Post-source decay, Plasma desorption, Surface-induced dissociation, Blackbody infrared radiative dissociation, Electron capture dissociation, Infrared multiphoton dissociation, Sustained off-resonance irradiation, High-energy collision-induced dissociation, Low-energy collision-induced dissociation, Photodissociation, Electron transfer dissociation, Pulsed q dissociation, trap-type collision-induced dissociation, beam-type collision-induced dissociation, in-source collision-induced dissociation, Bruker proprietary method

select_collision_energy: Select MSn scans with a collision energy in the given interval

select_isolation_window_width: Select MSn scans whose isolation window width is in the given interval

select_polarity Retain MSn scans with a certain scan polarityunknown, positive, negative

replace_pc_charge: Replaces in_charge with out_charge in all precursors.

++++blackorwhitelistBlack or white listing of of MS2 spectra by spectral similarity

file Input file containing MS2 spectra that should be retained or removed from the mzML file!
Matching tolerances are taken from 'spectra:blackorwhitelist:similarity_threshold|rt|mz' options.
input file*.mzML

similarity_threshold-1.0 Similarity threshold when matching MS2 spectra. (-1 = disabled).-1.0:1.0

rt0.01 Retention tolerance [s] when matching precursor positions. (-1 = disabled)

mz0.01 m/z tolerance [Th] when matching precursor positions. (-1 = disabled)

use_ppm_tolerancefalse If ppm tolerance should be used. Otherwise Da are used.

blacklisttrue True: remove matched MS2. False: retain matched MS2 spectra. Other levels are keptfalse, true

+++featureFeature data options

q: Overall quality range to extract [0:1]

+++consensusConsensus feature data options

map[] Non-empty list of maps to be extracted from a consensus (indices are 0-based).

map_andfalse Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')true, false

++++blackorwhitelistBlack or white listing of of MS2 spectra by consensus features

blacklisttrue True: remove matched MS2. False: retain matched MS2 spectra. Other levels are keptfalse, true

file Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file!
Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options.
If consensus:blackorwhitelist:maps is specified, only these will be used.
input file*.consensusXML

maps[] Maps used for black/white list filtering

rt60.0 Retention tolerance [s] for precursor to consensus feature position0.0:∞

mz0.01 m/z tolerance [Th] for precursor to consensus feature position0.0:∞

use_ppm_tolerancefalse If ppm tolerance should be used. Otherwise Da are used.false, true

+++f_and_cFeature & Consensus data options

charge: Charge range to extract

size: Size range to extract

remove_meta[] Expects a 3-tuple (=3 entries in the list), i.e. 'lt|eq|gt' ; the first is the name of meta value, followed by the comparison operator (equal, less or greater) 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!)!

remove_hullfalse Remove hull from features.true, false

+++idID options. The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -> remove_clashes -> keep_best_score_id -> sequences_whitelist / accessions_whitelist

remove_clashesfalse Remove features with id clashes (different sequences mapped to one feature)true, false

keep_best_score_idfalse in case of multiple peptide identifications, keep only the id with best scoretrue, false

sequences_whitelist[] Keep only features containing whitelisted substrings, e.g. features containing LYSNLVER or the modification (Oxidation). To control comparison method used for whitelisting, see 'id:sequence_comparison_method'.

sequence_comparison_methodsubstring Comparison method used to determine if a feature is whitelisted.substring, exact

accessions_whitelist[] keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN

remove_annotated_featuresfalse Remove features with annotationstrue, false

remove_unannotated_featuresfalse Remove features without annotationstrue, false

remove_unassigned_idsfalse Remove unassigned peptide identificationstrue, false

blacklist Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file!
Matching tolerances are taken from 'id:rt' and 'id:mz' options.
This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches.input file*.idXML

rt0.1 Retention tolerance [s] for precursor to id position0.0:∞

mz1.0e-03 m/z tolerance [Th] for precursor to id position0.0:∞

blacklist_imperfectfalse Allow for mismatching precursor positions (see 'id:blacklist')true, false

+++algorithmS/N algorithm section

++++SignalToNoise

max_intensity-1 maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.-1:∞

auto_max_stdev_factor3.0 parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev0.0:999.0

auto_max_percentile95 parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile0:100

auto_mode0 method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method-1:1

win_len200.0 window length in Thomson1.0:∞

bin_count30 number of bins for intensity values3:∞

min_required_elements10 minimum number of elements required in a window (otherwise it is considered sparse)1:∞

noise_for_empty_window1.0e20 noise value used for sparse windows

write_log_messagestrue Write out log messages in case of sparse windows or median in rightmost histogram bintrue, false

For the parameters of the S/N algorithm section see the class documentation there:
peak_options:sn