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required parameter

advanced parameter

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

version1.10.0 Version of the tool that generated this parameters file.

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

in input file input file*.mzML,*.featureXML,*.consensusXML

in_type input file type -- default: determined from file extension or content
mzML,featureXML,consensusXML

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

out_type output file type -- default: determined from file extension or content
mzML,featureXML,consensusXML

rt: retention time range to extract

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

pc_mz: 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.

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

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

+++peak_optionsPeak data options

sn0 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!

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

sort_peaksfalse sorts the peaks according to m/z.true,false

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

remove_chromatogramsfalse Removes chromatograms stored in a file.true,false

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

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

+++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 mode
Unknown,MassSpectrum,MS1Spectrum,MSnSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion

remove_activation Remove MSn scans where any of its precursors features a certain activation method
Collision-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

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,Absorbtion

select_activation Select MSn scans where any of its precursors features a certain activation method
Collision-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

+++featureFeature data options

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

+++consensusfeatureConsensus feature data options

map[] maps to be extracted from a consensus

map_andfalse AND connective of map selection instead of OR.true,false

+++f_and_cfFeature & 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!)!

+++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 with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)

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:∞

mz0.001 m/z tolerance [Th] for precursor to id position0:∞

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 parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev0:999

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 window length in Thomson1:∞

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_window1e+20 noise value used for sparse windows