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mzmine_params.xml
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<?xml version="1.0" encoding="UTF-8"?><batch mzmine_version="3.9.0">
<batchstep method="io.github.mzmine.modules.dataprocessing.featdet_massdetection.MassDetectionModule" parameter_version="1">
<parameter name="Raw data files" type="GUI_SELECTED_FILES"/>
<parameter name="Scan filters" selected="true">
<parameter name="Scan number"/>
<parameter name="Base Filtering Integer"/>
<parameter name="Retention time"/>
<parameter name="Mobility"/>
<parameter name="MS level filter" selected="MS1, level = 1">1</parameter>
<parameter name="Scan definition"/>
<parameter name="Polarity">Any</parameter>
<parameter name="Spectrum type">ANY</parameter>
</parameter>
<parameter name="Scan types (IMS)">All scan types</parameter>
<parameter name="Mass detector" selected_item="Centroid">
<module name="Factor of lowest signal">
<parameter name="Noise factor">2.5</parameter>
</module>
<module name="Centroid">
<parameter name="Noise level">6000.0</parameter>
<parameter name="Detect isotope signals below noise level" selected="false">
<parameter name="Chemical elements">H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>5.0E-4</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Maximum charge of isotope m/z">1</parameter>
</parameter>
</module>
<module name="Exact mass">
<parameter name="Noise level"/>
<parameter name="Detect isotope signals below noise level" selected="false">
<parameter name="Chemical elements">H,C,N,O,S</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>5.0E-4</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Maximum charge of isotope m/z">1</parameter>
</parameter>
</module>
<module name="Local maxima">
<parameter name="Noise level"/>
</module>
<module name="Recursive threshold">
<parameter name="Noise level"/>
<parameter name="Min m/z peak width"/>
<parameter name="Max m/z peak width"/>
</module>
<module name="Wavelet transform">
<parameter name="Noise level"/>
<parameter name="Scale level"/>
<parameter name="Wavelet window size (%)"/>
</module>
<module name="Auto">
<parameter name="Noise level">1000.0</parameter>
<parameter name="Detect isotope signals below noise level" selected="false">
<parameter name="Chemical elements">H,C,N,O,S</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>5.0E-4</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Maximum charge of isotope m/z">1</parameter>
</parameter>
</module>
</parameter>
<parameter name="Denormalize fragment scans (traps)">false</parameter>
<parameter name="Output netCDF filename (optional)" selected="false"/>
</batchstep>
<batchstep method="io.github.mzmine.modules.dataprocessing.featdet_massdetection.MassDetectionModule" parameter_version="1">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Scan filters" selected="true">
<parameter name="Scan number"/>
<parameter name="Base Filtering Integer"/>
<parameter name="Retention time"/>
<parameter name="Mobility"/>
<parameter name="MS level filter" selected="MS2, level = 2">1</parameter>
<parameter name="Scan definition"/>
<parameter name="Polarity">Any</parameter>
<parameter name="Spectrum type">ANY</parameter>
</parameter>
<parameter name="Scan types (IMS)">All scan types</parameter>
<parameter name="Mass detector" selected_item="Centroid">
<module name="Factor of lowest signal">
<parameter name="Noise factor">2.5</parameter>
</module>
<module name="Centroid">
<parameter name="Noise level">30.0</parameter>
<parameter name="Detect isotope signals below noise level" selected="false">
<parameter name="Chemical elements">H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>5.0E-4</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Maximum charge of isotope m/z">1</parameter>
</parameter>
</module>
<module name="Exact mass">
<parameter name="Noise level"/>
<parameter name="Detect isotope signals below noise level" selected="false">
<parameter name="Chemical elements">H,C,N,O,S</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>5.0E-4</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Maximum charge of isotope m/z">1</parameter>
</parameter>
</module>
<module name="Local maxima">
<parameter name="Noise level"/>
</module>
<module name="Recursive threshold">
<parameter name="Noise level"/>
<parameter name="Min m/z peak width"/>
<parameter name="Max m/z peak width"/>
</module>
<module name="Wavelet transform">
<parameter name="Noise level"/>
<parameter name="Scale level"/>
<parameter name="Wavelet window size (%)"/>
</module>
<module name="Auto">
<parameter name="Noise level">1000.0</parameter>
<parameter name="Detect isotope signals below noise level" selected="false">
<parameter name="Chemical elements">H,C,N,O,S</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>5.0E-4</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Maximum charge of isotope m/z">1</parameter>
</parameter>
</module>
</parameter>
<parameter name="Denormalize fragment scans (traps)">false</parameter>
<parameter name="Output netCDF filename (optional)" selected="false"/>
</batchstep>
<batchstep method="io.github.mzmine.modules.dataprocessing.featdet_adapchromatogrambuilder.ModularADAPChromatogramBuilderModule" parameter_version="1">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Scan filters" selected="true">
<parameter name="Scan number"/>
<parameter name="Base Filtering Integer"/>
<parameter name="Retention time"/>
<parameter name="Mobility"/>
<parameter name="MS level filter" selected="MS1, level = 1">1</parameter>
<parameter name="Scan definition"/>
<parameter name="Polarity">Any</parameter>
<parameter name="Spectrum type">ANY</parameter>
</parameter>
<parameter name="Minimum consecutive scans">4</parameter>
<parameter name="Minimum intensity for consecutive scans">6000.0</parameter>
<parameter name="Minimum absolute height">12000.0</parameter>
<parameter name="m/z tolerance (scan-to-scan)">
<absolutetolerance>0.0</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Suffix">chromatograms</parameter>
<parameter name="Allow single scan chromatograms"/>
</batchstep>
<batchstep method="io.github.mzmine.modules.dataprocessing.featdet_chromatogramdeconvolution.minimumsearch.MinimumSearchFeatureResolverModule" parameter_version="2">
<parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>
<parameter name="Suffix">resolved</parameter>
<parameter name="Original feature list">REMOVE</parameter>
<parameter name="MS/MS scan pairing" selected="true">
<parameter name="MS1 to MS2 precursor tolerance (m/z)">
<absolutetolerance>0.01</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Retention time filter" selected="Use feature edges" unit="MINUTES">0.2</parameter>
<parameter name="Minimum relative feature height" selected="true">0.25</parameter>
<parameter name="Minimum required signals" selected="true">1</parameter>
<parameter name="Limit by ion mobility edges">false</parameter>
<parameter name="Merge MS/MS spectra (TIMS)">false</parameter>
<parameter name="Minimum signal intensity (absolute, TIMS)" selected="false">250.0</parameter>
<parameter name="Minimum signal intensity (relative, TIMS)" selected="true">0.01</parameter>
</parameter>
<parameter name="Dimension">Retention time</parameter>
<parameter name="Chromatographic threshold">0.95</parameter>
<parameter name="Minimum search range RT/Mobility (absolute)">1.0</parameter>
<parameter name="Minimum relative height">0.01</parameter>
<parameter name="Minimum absolute height">1000.0</parameter>
<parameter name="Min ratio of peak top/edge">0.0</parameter>
<parameter name="Peak duration range (min/mobility)">
<min>0.0</min>
<max>1.0</max>
</parameter>
<parameter name="Minimum scans (data points)">4</parameter>
</batchstep>
<batchstep method="io.github.mzmine.modules.dataprocessing.filter_isotopegrouper.IsotopeGrouperModule" parameter_version="1">
<parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>
<parameter name="Name suffix">deisotoped</parameter>
<parameter name="m/z tolerance (intra-sample)">
<absolutetolerance>0.0</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Retention time tolerance" unit="MINUTES">0.15</parameter>
<parameter name="Mobility tolerance" selected="false"/>
<parameter name="Monotonic shape">false</parameter>
<parameter name="Maximum charge">2</parameter>
<parameter name="Representative isotope">Most intense</parameter>
<parameter name="Never remove feature with MS2">false</parameter>
<parameter name="Original feature list">REMOVE</parameter>
</batchstep>
<batchstep method="io.github.mzmine.modules.dataprocessing.filter_rowsfilter.RowsFilterModule" parameter_version="2">
<parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>
<parameter name="Name suffix">filtered</parameter>
<parameter name="Minimum aligned features (samples)" selected="false">
<abs>1</abs>
<rel>0.0</rel>
</parameter>
<parameter name="Minimum features in an isotope pattern" selected="false">2</parameter>
<parameter name="Validate 13C isotope pattern" selected="false">
<parameter name="m/z tolerance">
<absolutetolerance>5.0E-4</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Max charge">1</parameter>
<parameter name="Estimate minimum carbon">true</parameter>
<parameter name="Remove if 13C">true</parameter>
<parameter name="Exclude isotopes">H,C,N,O,S,H,C,N,O,S,H,C,N,O,S,H,C,N,O,S</parameter>
</parameter>
<parameter name="Remove redundant isotope rows">false</parameter>
<parameter name="m/z" selected="false"/>
<parameter name="Retention time" selected="false">
<min>0.0</min>
<max>12.0</max>
</parameter>
<parameter name="features duration range" selected="false">
<min>0.0</min>
<max>3.0</max>
</parameter>
<parameter name="Chromatographic FWHM" selected="false">
<min>0.0</min>
<max>1.0</max>
</parameter>
<parameter name="Charge" selected="false">
<min>1</min>
<max>2</max>
</parameter>
<parameter name="Kendrick mass defect" selected="false">
<parameter name="Kendrick mass defect">
<min>0.0</min>
<max>1.0</max>
</parameter>
<parameter name="Kendrick mass base"/>
<parameter name="Shift">0.0</parameter>
<parameter name="Charge">1</parameter>
<parameter name="Divisor">1</parameter>
<parameter name="Use Remainder of Kendrick mass">false</parameter>
</parameter>
<parameter name="Parameter">No parameters defined</parameter>
<parameter name="Only identified?">false</parameter>
<parameter name="Text in identity" selected="false"/>
<parameter name="Text in comment" selected="false"/>
<parameter name="Keep or remove rows">Keep rows that match all criteria</parameter>
<parameter name="Feature with MS2 scan">true</parameter>
<parameter name="Never remove feature with MS2">false</parameter>
<parameter name="Reset the feature number ID">true</parameter>
<parameter name="Mass defect" selected="false"/>
<parameter name="Original feature list">REMOVE</parameter>
</batchstep>
</batch>