/
batchQE-MZmine-2.33.xml
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batchQE-MZmine-2.33.xml
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<?xml version="1.0" encoding="UTF-8"?>
<batch>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule">
<parameter name="Raw data file names">
<file>/Users/priya/Desktop/protocode/testdata/aMCA_1-10.mzXML</file>
<file>/Users/priya/Desktop/protocode/testdata/bMCA_1-10.mzXML</file>
<file>/Users/priya/Desktop/protocode/testdata/CA_1-10.mzXML</file>
<file>/Users/priya/Desktop/protocode/testdata/CLA_1-2.mzXML</file>
<file>/Users/priya/Desktop/protocode/testdata/Ellaidic_acid_1-2.mzXML</file>
<file>/Users/priya/Desktop/protocode/testdata/END_1-10.mzXML</file>
<file>/Users/priya/Desktop/protocode/testdata/ENL_1-10.mzXML</file>
<file>/Users/priya/Desktop/protocode/testdata/LA_1-2.mzXML</file>
<file>/Users/priya/Desktop/protocode/testdata/Oleic_1-10.mzXML</file>
<file>/Users/priya/Desktop/protocode/testdata/Phytomonic_1-10.mzXML</file>
</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule">
<parameter name="Raw data files" type="ALL_FILES"/>
<parameter name="Scans">
<ms_level>1</ms_level>
<scan_definition/>
</parameter>
<parameter name="Mass detector" selected="Centroid">
<module name="Centroid">
<parameter name="Noise level">200000.0</parameter>
</module>
<module name="Exact mass">
<parameter name="Noise level"/>
</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>
</parameter>
<parameter name="Mass list name">masses</parameter>
<parameter name="CDF Filename (optional)" selected="false"/>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule">
<parameter name="Raw data files" type="ALL_FILES"/>
<parameter name="Scans">
<ms_level>2</ms_level>
<scan_definition/>
</parameter>
<parameter name="Mass detector" selected="Centroid">
<module name="Centroid">
<parameter name="Noise level">1000.0</parameter>
</module>
<module name="Exact mass">
<parameter name="Noise level"/>
</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>
</parameter>
<parameter name="Mass list name">masses</parameter>
<parameter name="CDF Filename (optional)" selected="false"/>
</batchstep>
<batchstep method="net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderModule">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Scans">
<ms_level>1</ms_level>
</parameter>
<parameter name="Mass list">masses</parameter>
<parameter name="Min time span (min)">0.05</parameter>
<parameter name="Min height">1000000.0</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>1.0E-4</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Suffix">chromatograms</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.DeconvolutionModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Suffix">deconvoluted</parameter>
<parameter name="Algorithm" selected="Local minimum search">
<module name="Baseline cut-off">
<parameter name="Min peak height">6000.0</parameter>
<parameter name="Peak duration range (min)">
<min>0.02</min>
<max>3.0</max>
</parameter>
<parameter name="Baseline level">2000.0</parameter>
</module>
<module name="Noise amplitude">
<parameter name="Min peak height"/>
<parameter name="Peak duration range (min)">
<min>0.0</min>
<max>10.0</max>
</parameter>
<parameter name="Amplitude of noise"/>
</module>
<module name="Savitzky-Golay">
<parameter name="Min peak height"/>
<parameter name="Peak duration range (min)">
<min>0.0</min>
<max>10.0</max>
</parameter>
<parameter name="Derivative threshold level"/>
</module>
<module name="Local minimum search">
<parameter name="Chromatographic threshold">0.01</parameter>
<parameter name="Search minimum in RT range (min)">0.01</parameter>
<parameter name="Minimum relative height">0.01</parameter>
<parameter name="Minimum absolute height">1000000.0</parameter>
<parameter name="Min ratio of peak top/edge">3.0</parameter>
<parameter name="Peak duration range (min)">
<min>0.05</min>
<max>1.0</max>
</parameter>
</module>
<module name="Wavelets (XCMS)">
<parameter name="S/N threshold">10.0</parameter>
<parameter name="Wavelet scales">
<min>0.25</min>
<max>5.0</max>
</parameter>
<parameter name="Peak duration range">
<min>0.0</min>
<max>10.0</max>
</parameter>
<parameter name="Peak integration method">Use smoothed data</parameter>
<parameter name="R engine">RCaller</parameter>
</module>
<module name="Wavelets (ADAP)">
<parameter name="S/N threshold">10.0</parameter>
<parameter name="S/N estimator">
<module name="Intensity window SN"/>
<module name="Wavelet Coeff. SN">
<parameter name="Peak width mult.">3.0</parameter>
<parameter name="abs(wavelet coeffs.)">true</parameter>
</module>
</parameter>
<parameter name="min feature height">10.0</parameter>
<parameter name="coefficient/area threshold">110.0</parameter>
<parameter name="Peak duration range">
<min>0.0</min>
<max>10.0</max>
</parameter>
<parameter name="RT wavelet range">
<min>0.001</min>
<max>0.1</max>
</parameter>
</module>
</parameter>
<parameter name="m/z range for MS2 scan pairing (Da)" selected="true">0.001</parameter>
<parameter name="RT range for MS2 scan pairing (min)" selected="true">0.1</parameter>
<parameter name="Remove original peak list">true</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.isotopes.deisotoper.IsotopeGrouperModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Name suffix">deisotoped</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>1.0E-4</absolutetolerance>
<ppmtolerance>15.0</ppmtolerance>
</parameter>
<parameter name="Retention time tolerance" type="absolute">0.05</parameter>
<parameter name="Monotonic shape">false</parameter>
<parameter name="Maximum charge">3</parameter>
<parameter name="Representative isotope">Most intense</parameter>
<parameter name="Remove original peaklist">true</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.alignment.join.JoinAlignerModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Peak list name">Aligned</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>1.0E-4</absolutetolerance>
<ppmtolerance>10.0</ppmtolerance>
</parameter>
<parameter name="Weight for m/z">75.0</parameter>
<parameter name="Retention time tolerance" type="absolute">0.05</parameter>
<parameter name="Weight for RT">25.0</parameter>
<parameter name="Require same charge state">false</parameter>
<parameter name="Require same ID">false</parameter>
<parameter name="Compare isotope pattern" selected="false">
<parameter name="Isotope m/z tolerance">
<absolutetolerance>0.001</absolutetolerance>
<ppmtolerance>5.0</ppmtolerance>
</parameter>
<parameter name="Minimum absolute intensity"/>
<parameter name="Minimum score"/>
</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.gapfilling.peakfinder.PeakFinderModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Name suffix">gap-filled</parameter>
<parameter name="Intensity tolerance">0.1</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>1.0E-4</absolutetolerance>
<ppmtolerance>15.0</ppmtolerance>
</parameter>
<parameter name="Retention time tolerance" type="absolute">0.1</parameter>
<parameter name="RT correction">false</parameter>
<parameter name="Remove original peak list">false</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.filtering.rowsfilter.RowsFilterModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Name suffix">filtered_3_2</parameter>
<parameter name="Minimum peaks in a row" selected="true">3.0</parameter>
<parameter name="Minimum peaks in an isotope pattern" selected="true">2</parameter>
<parameter name="m/z" selected="false"/>
<parameter name="Retention time" selected="false"/>
<parameter name="Peak duration range" selected="false">
<min>0.0</min>
<max>10.0</max>
</parameter>
<parameter name="Chromatographic FWHM" selected="false">
<min>0.0</min>
<max>1.0</max>
</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="Keep only peaks with MS2 scan (GNPS)">false</parameter>
<parameter name="Reset the peak number ID">false</parameter>
<parameter name="Remove source peak list after filtering">false</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.filtering.duplicatefilter.DuplicateFilterModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Name suffix">filtered</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>1.0E-4</absolutetolerance>
<ppmtolerance>5.0</ppmtolerance>
</parameter>
<parameter name="RT tolerance" type="absolute">0.05</parameter>
<parameter name="Require same identification">false</parameter>
<parameter name="Remove original peaklist">false</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.filtering.rowsfilter.RowsFilterModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Name suffix">filtered_MS2</parameter>
<parameter name="Minimum peaks in a row" selected="false"/>
<parameter name="Minimum peaks in an isotope pattern" selected="false"/>
<parameter name="m/z" selected="false"/>
<parameter name="Retention time" selected="false"/>
<parameter name="Peak duration range" selected="false">
<min>0.0</min>
<max>10.0</max>
</parameter>
<parameter name="Chromatographic FWHM" selected="false">
<min>0.0</min>
<max>1.0</max>
</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="Keep only peaks with MS2 scan (GNPS)">true</parameter>
<parameter name="Reset the peak number ID">true</parameter>
<parameter name="Remove source peak list after filtering">false</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.io.csvexport.CSVExportModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Filename">/Users/priya/Desktop/test.csv</parameter>
<parameter name="Field separator">,</parameter>
<parameter name="Export common elements">
<item>Export row ID</item>
<item>Export row m/z</item>
<item>Export row retention time</item>
</parameter>
<parameter name="Export data file elements">
<item>Peak area</item>
</parameter>
<parameter name="Export quantitation results and other information">false</parameter>
<parameter name="Identification separator">;</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.io.gnpsexport.GNPSExportModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Filename">/Users/priya/Desktop/test_gnps.mgf</parameter>
<parameter name="Mass list">masses</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.io.siriusexport.SiriusExportModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Filename">/Users/priya/Desktop/test_sirius.mgf</parameter>
<parameter name="Merge mode">Merge consecutive scans</parameter>
<parameter name="Mass list">masses</parameter>
</batchstep>
</batch>