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<div class="title">FileFilter </div> </div>
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<div class="textblock"><p>Extracts portions of the data from an mzML, featureXML or consensusXML file. </p>
<center></center><center><table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> FileFilter <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1">any tool yielding output <br/>
in mzML, featureXML <br/>
or consensusXML format </td><td valign="middle" align="center" rowspan="1"><p class="starttd">any tool that profits on reduced input </p>
<p class="endtd"></p>
</td></tr>
</table>
</center><p> 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.</p>
<p>Depending on the input file type, additional specific operations are possible:</p>
<ul>
<li>mzML<ul>
<li>extract spectra of a certain MS level</li>
<li>filter by signal-to-noise estimation</li>
<li>filter by scan mode of the spectra</li>
</ul>
</li>
<li>remove MS2 scans whose precursor matches identifications (from an idXML file in 'id:blacklist')</li>
<li>featureXML<ul>
<li>filter by feature charge</li>
<li>filter by feature size (number of subordinate features)</li>
<li>filter by overall feature quality</li>
</ul>
</li>
<li>consensusXML<ul>
<li>filter by size (number of elements in consensus features)</li>
<li>filter by consensus feature charge</li>
<li>filter by map (extracts specified maps and re-evaluates consensus centroid)<br/>
e.g. FileFilter -map 2 3 5 -in file1.consensusXML -out file2.consensusXML<br/>
If a single map is specified, the feature itself can be extracted.<br/>
e.g. FileFilter -map 5 -in file1.consensusXML -out file2.featureXML</li>
</ul>
</li>
<li>featureXML / consensusXML:</li>
<li>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.<ul>
<li>filter sequences, e.g. "LYSNLVER" or the modification "(Phospho)"<br/>
e.g. FileFilter -id:sequences_whitelist Phospho -in file1.consensusXML -out file2.consensusXML</li>
<li>filter accessions, e.g. "sp|P02662|CASA1_BOVIN"</li>
<li>remove features with annotations</li>
<li>remove features without annotations</li>
<li>remove unassigned peptide identifications</li>
<li>filter id with best score of features with multiple peptide identifications<br/>
e.g. FileFilter -id:remove_unannotated_features -id:remove_unassigned_ids -id:keep_best_score_id -in file1.featureXML -out file2.featureXML</li>
<li>remove features with id clashes (different sequences mapped to one feature)</li>
</ul>
</li>
</ul>
<p>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</p>
<p>MS2 and higher spectra can be filtered according to precursor m/z (see 'pc_mz'). 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 and use 'mz' option for MS1 and 'pc_mz' for MS2 data. Then merge them again. RT can be filtered at any step.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
FileFilter -- Extracts or manipulates portions of data from peak, feature or consensus-feature files.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
FileFilter <options>
This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.
Options (mandatory options marked with '*'):
-in <file>* Input file (valid formats: 'mzML', 'featureXML', 'cons
ensusXML')
-in_type <type> Input file type -- default: determined from file extens
ion or content
(valid: 'mzML', 'featureXML', 'consensusXML')
-out <file>* Output file (valid formats: 'mzML', 'featureXML', 'cons
ensusXML')
-out_type <type> Output file type -- default: determined from file exten
sion or content
(valid: 'mzML', 'featureXML', 'consensusXML')
-rt [min]:[max] Retention time range to extract (default: ':')
-mz [min]:[max] M/z range to extract (applies to ALL ms levels!) (defau
lt: ':')
-pc_mz [min]:[max] 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 compati
ble with this flag. (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 (default: '0')
-peak_options:rm_pc_charge i j ... Remove MS(2) spectra with these precursor charges. All
spectra without precursor are 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 chromatograms, e.g.
from SRM scans.
-peak_options:remove_chromatograms Removes chromatograms stored in a file.
-peak_options:mz_precision 32 or 64 Store base64 encoded m/z data using 32 or 64 bit precis
ion. (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')
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', 'MS
nSpectrum', 'SelectedIonMonitoring', 'SelectedReactionM
onitoring', 'ConsecutiveReactionMonitoring', 'ConstantN
eutralGain', 'ConstantNeutralLoss', 'Precursor', 'Enhan
cedMultiplyCharged', 'TimeDelayedFragmentation', 'Elect
romagneticRadiation', 'Emission', 'Absorbtion')
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-sourc
e decay', 'Plasma desorption', 'Surface-induced dissoci
ation', 'Blackbody infrared radiative dissociation',
'Electron capture dissociation', 'Infrared multiphoton
dissociation', 'Sustained off-resonance irradiation',
'High-energy collision-induced dissociation', 'Low-ener
...
ion')
-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 whichs 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', 'MS1Spectrum', 'MS
nSpectrum', 'SelectedIonMonitoring', 'SelectedReactionM
onitoring', 'ConsecutiveReactionMonitoring', 'ConstantN
eutralGain', 'ConstantNeutralLoss', 'Precursor', 'Enhan
cedMultiplyCharged', 'TimeDelayedFragmentation', 'Elect
romagneticRadiation', 'Emission', 'Absorbtion')
-spectra:select_activation <activation> Select MSn scans where any of its precursors features
a certain activation method
(valid: 'Collision-induced dissociation', 'Post-sourc
e decay', 'Plasma desorption', 'Surface-induced dissoci
ation', 'Blackbody infrared radiative dissociation',
'Electron capture dissociation', 'Infrared multiphoton
dissociation', 'Sustained off-resonance irradiation',
'High-energy collision-induced dissociation', 'Low-ener
...
ion')
-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 whichs isolation window width is in
the given interval. (default: ':')
Feature data options:
-feature:q [min]:[max] Overall quality range to extract [0:1] (default: ':')
Consensus feature data options:
-consensus:map i j ... Maps to be extracted from a consensus
-consensus:map_and Consensus features are kept only if they contain exactl
y 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 matched MS2
spectra. Other levels are kept. (default: 'true' valid:
'false', 'true')
-consensus:blackorwhitelist:file <file> Input file containing consensus features whose correspo
nding MS2 spectra should be removed from the mzML file!
Matching tolerances are taken from 'consensus:blackorw
hitelist:rt' and 'consensus:blackorwhitelist:mz' option
s.
If consensus:blackorwhitelist:maps is specified, 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 consensus feat
ure position (default: '60' min: '0')
-consensus:blackorwhitelist:mz tolerance M/z tolerance [Th] for precursor to consensus feature
position (default: '0.01' min: '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 valu
e, 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 corres
ponding data value type of the meta value (for lists,
this simply compares length, not content!)!
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 with white listed sequences, e.g.
LYSNLVER or the modification (Oxidation)
-id:accessions_whitelist <accessions> Keep only features with white listed accessions, 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 whose corresp
onding 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:black
list_imperfect' to allow for mismatches. (valid formats
: 'idXML')
-id:rt tolerance Retention tolerance [s] for precursor to id position
(default: '0.1' min: '0')
-id:mz tolerance M/z tolerance [Th] for precursor to id position (defaul
t: '0.001' min: '0')
-id:blacklist_imperfect Allow for mismatching precursor positions (see 'id:blac
klist')
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.
Have a look at the OpenMS documentation for more information.
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+FileFilter</span><span class="node_description">Extracts or manipulates portions of data from peak, feature or consensus-feature files.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'FileFilter'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">input file </span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML,*.featureXML,*.consensusXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">in_type</span><span class="item_value"></span>
<span class="item_description">input file type -- default: determined from file extension or content<br></span><span class="item_tags"></span><span class="item_restrictions">mzML,featureXML,consensusXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">output file</span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML,*.featureXML,*.consensusXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out_type</span><span class="item_value"></span>
<span class="item_description">output file type -- default: determined from file extension or content<br></span><span class="item_tags"></span><span class="item_restrictions">mzML,featureXML,consensusXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">rt</span><span class="item_value">:</span>
<span class="item_description">retention time range to extract</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">mz</span><span class="item_value">:</span>
<span class="item_description">m/z range to extract (applies to ALL ms levels!)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">pc_mz</span><span class="item_value">:</span>
<span class="item_description">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.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">int</span><span class="item_value">:</span>
<span class="item_description">intensity range to extract</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">sort</span><span class="item_value">false</span>
<span class="item_description">sorts the output according to RT and m/z.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">+++peak_options</span><span class="node_description">Peak data options</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">sn</span><span class="item_value">0</span>
<span class="item_description">write peaks with S/N > 'sn' values only</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">rm_pc_charge</span><span class="item_value">[]</span>
<span class="item_description">Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">level</span><span class="item_value">[1, 2, 3]</span>
<span class="item_description">MS levels to extract</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">sort_peaks</span><span class="item_value">false</span>
<span class="item_description">sorts the peaks according to m/z.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">no_chromatograms</span><span class="item_value">false</span>
<span class="item_description">No conversion to space-saving real chromatograms, e.g. from SRM scans.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">remove_chromatograms</span><span class="item_value">false</span>
<span class="item_description">Removes chromatograms stored in a file.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">mz_precision</span><span class="item_value">64</span>
<span class="item_description">Store base64 encoded m/z data using 32 or 64 bit precision.</span><span class="item_tags"></span><span class="item_restrictions">32,64</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">int_precision</span><span class="item_value">32</span>
<span class="item_description">Store base64 encoded intensity data using 32 or 64 bit precision.</span><span class="item_tags"></span><span class="item_restrictions">32,64</span></div> <div class="node"><span class="node_name">+++spectra</span><span class="node_description">Remove spectra or select spectra (removing all others) with certain properties.</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">remove_zoom</span><span class="item_value">false</span>
<span class="item_description">Remove zoom (enhanced resolution) scans</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">remove_mode</span><span class="item_value"></span>
<span class="item_description">Remove scans by scan mode<br></span><span class="item_tags"></span><span class="item_restrictions">Unknown,MassSpectrum,MS1Spectrum,MSnSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">remove_activation</span><span class="item_value"></span>
<span class="item_description">Remove MSn scans where any of its precursors features a certain activation method<br></span><span class="item_tags"></span><span class="item_restrictions">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</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">remove_collision_energy</span><span class="item_value">:</span>
<span class="item_description">Remove MSn scans with a collision energy in the given interval.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">remove_isolation_window_width</span><span class="item_value">:</span>
<span class="item_description">Remove MSn scans whichs isolation window width is in the given interval.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">select_zoom</span><span class="item_value">false</span>
<span class="item_description">Select zoom (enhanced resolution) scans</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">select_mode</span><span class="item_value"></span>
<span class="item_description">Selects scans by scan mode<br></span><span class="item_tags"></span><span class="item_restrictions">Unknown,MassSpectrum,MS1Spectrum,MSnSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorbtion</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">select_activation</span><span class="item_value"></span>
<span class="item_description">Select MSn scans where any of its precursors features a certain activation method<br></span><span class="item_tags"></span><span class="item_restrictions">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</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">select_collision_energy</span><span class="item_value">:</span>
<span class="item_description">Select MSn scans with a collision energy in the given interval.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">select_isolation_window_width</span><span class="item_value">:</span>
<span class="item_description">Select MSn scans whichs isolation window width is in the given interval.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">+++feature</span><span class="node_description">Feature data options</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">q</span><span class="item_value">:</span>
<span class="item_description">Overall quality range to extract [0:1]</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">+++consensus</span><span class="node_description">Consensus feature data options</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">map</span><span class="item_value">[]</span>
<span class="item_description">maps to be extracted from a consensus</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">map_and</span><span class="item_value">false</span>
<span class="item_description">Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map').</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">++++blackorwhitelist</span><span class="node_description">Black or white listing of of MS2 spectra by consensus features.</span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">blacklist</span><span class="item_value">true</span>
<span class="item_description">True: remove matched MS2. False: retain matched MS2 spectra. Other levels are kept.</span><span class="item_tags"></span><span class="item_restrictions">false,true</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">file</span><span class="item_value"></span>
<span class="item_description">Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file!<br>Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options.<br>If consensus:blackorwhitelist:maps is specified, only these will be used.<br></span><span class="item_tags">input file</span><span class="item_restrictions">*.consensusXML</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">maps</span><span class="item_value">[]</span>
<span class="item_description">maps used for black/white list filtering.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">rt</span><span class="item_value">60</span>
<span class="item_description">retention tolerance [s] for precursor to consensus feature position</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">mz</span><span class="item_value">0.01</span>
<span class="item_description">m/z tolerance [Th] for precursor to consensus feature position</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">use_ppm_tolerance</span><span class="item_value">false</span>
<span class="item_description">If ppm tolerance should be used. Otherwise Da are used.</span><span class="item_tags"></span><span class="item_restrictions">false,true</span></div> <div class="node"><span class="node_name">+++f_and_c</span><span class="node_description">Feature & Consensus data options</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">charge</span><span class="item_value">:</span>
<span class="item_description">charge range to extract</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">size</span><span class="item_value">:</span>
<span class="item_description">size range to extract</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">remove_meta</span><span class="item_value">[]</span>
<span class="item_description">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 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!)!</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">+++id</span><span class="node_description">ID options. The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -> remove_clashes -> keep_best_score_id -> sequences_whitelist / accessions_whitelist.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:32px;">remove_clashes</span><span class="item_value">false</span>
<span class="item_description">remove features with id clashes (different sequences mapped to one feature)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">keep_best_score_id</span><span class="item_value">false</span>
<span class="item_description">in case of multiple peptide identifications, keep only the id with best score</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">sequences_whitelist</span><span class="item_value">[]</span>
<span class="item_description">keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">accessions_whitelist</span><span class="item_value">[]</span>
<span class="item_description">keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">remove_annotated_features</span><span class="item_value">false</span>
<span class="item_description">remove features with annotations</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">remove_unannotated_features</span><span class="item_value">false</span>
<span class="item_description">remove features without annotations</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">remove_unassigned_ids</span><span class="item_value">false</span>
<span class="item_description">remove unassigned peptide identifications</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">blacklist</span><span class="item_value"></span>
<span class="item_description">Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file!<br>Matching tolerances are taken from 'id:rt' and 'id:mz' options.<br>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.</span><span class="item_tags">input file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">rt</span><span class="item_value">0.1</span>
<span class="item_description">retention tolerance [s] for precursor to id position</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">mz</span><span class="item_value">0.001</span>
<span class="item_description">m/z tolerance [Th] for precursor to id position</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">blacklist_imperfect</span><span class="item_value">false</span>
<span class="item_description">Allow for mismatching precursor positions (see 'id:blacklist')</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">+++algorithm</span><span class="node_description">S/N algorithm section</span></div>
<div class="node"><span class="node_name">++++SignalToNoise</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:40px;">max_intensity</span><span class="item_value">-1</span>
<span class="item_description">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.</span><span class="item_tags"></span><span class="item_restrictions">-1:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">auto_max_stdev_factor</span><span class="item_value">3</span>
<span class="item_description">parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev</span><span class="item_tags"></span><span class="item_restrictions">0:999</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">auto_max_percentile</span><span class="item_value">95</span>
<span class="item_description">parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile</span><span class="item_tags"></span><span class="item_restrictions">0:100</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">auto_mode</span><span class="item_value">0</span>
<span class="item_description">method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method</span><span class="item_tags"></span><span class="item_restrictions">-1:1</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">win_len</span><span class="item_value">200</span>
<span class="item_description">window length in Thomson</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">bin_count</span><span class="item_value">30</span>
<span class="item_description">number of bins for intensity values</span><span class="item_tags"></span><span class="item_restrictions">3:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">min_required_elements</span><span class="item_value">10</span>
<span class="item_description">minimum number of elements required in a window (otherwise it is considered sparse)</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:40px;">noise_for_empty_window</span><span class="item_value">1e+20</span>
<span class="item_description">noise value used for sparse windows</span><span class="item_tags"></span><span class="item_restrictions"> </span></div></div>
<p>For the parameters of the S/N algorithm section see the class documentation there: <br/>
<a class="el" href="classOpenMS_1_1SignalToNoiseEstimatorMedian.html">peak_options:sn</a><br/>
</p>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000031">Todo:</a></b></dt><dd>add tests for selecting modes (port remove modes) (Andreas) </dd></dl>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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