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Added batch mode for clustering
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- Cleaned up folders
- added clustering workflow
- MZmine version 2.41.6-imzml
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@robinschmid
robinschmid committed May 15, 2020
1 parent 3042434 commit 66a07c5
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Showing 6 changed files with 563 additions and 204 deletions.
334 changes: 167 additions & 167 deletions 20190805_batch_full_peaklist.xml → ...ocessing/20190805_batch_full_peaklist.xml
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Original file line number Diff line number Diff line change
@@ -1,167 +1,167 @@
<?xml version="1.0" encoding="UTF-8"?>
<batch>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesModule">
<parameter name="Raw data files" type="ALL_FILES"/>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.merge.RawFileMergeModule">
<parameter name="Raw data files" type="ALL_FILES"/>
<parameter name="Mode">MERGE SELECTED</parameter>
<parameter name="Grouping identifier position">AFTER LAST</parameter>
<parameter name="Position marker">_</parameter>
<parameter name="MS2 marker" selected="false"/>
<parameter name="Suffix to new name">_merged</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.filtering.scanfilters.ScanFiltersModule">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Scans"/>
<parameter name="Suffix">filtered</parameter>
<parameter name="Filter" selected="Savitzky-Golay filter">
<module name="Savitzky-Golay filter">
<parameter name="Number of datapoints">9</parameter>
</module>
<module name="Mean filter">
<parameter name="Window length"/>
</module>
<module name="Resampling filter">
<parameter name="m/z bin length"/>
</module>
<module name="Round resampling filter">
<parameter name="Sum duplicate intensities">false</parameter>
<parameter name="Remove zero intensity m/z peaks">true</parameter>
</module>
</parameter>
<parameter name="Remove source file after filtering">false</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Scans">
<ms_level>1</ms_level>
<scan_definition/>
</parameter>
<parameter name="Mass detector" selected="Exact mass">
<module name="Centroid">
<parameter name="Noise level">100.0</parameter>
</module>
<module name="Exact mass">
<parameter name="Noise level">300.0</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>
</parameter>
<parameter name="Mass list name">masses</parameter>
<parameter name="Output netCDF filename (optional)" selected="false"/>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Scans">
<ms_level>2</ms_level>
<scan_definition/>
</parameter>
<parameter name="Mass detector" selected="Exact mass">
<module name="Centroid">
<parameter name="Noise level">100.0</parameter>
</module>
<module name="Exact mass">
<parameter name="Noise level">120.0</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>
</parameter>
<parameter name="Mass list name">masses</parameter>
<parameter name="Output netCDF filename (optional)" selected="false"/>
</batchstep>
<batchstep method="net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterModule">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Mass list">masses</parameter>
<parameter name="Mass resolution">15000.0</parameter>
<parameter name="Peak model function">Lorentzian</parameter>
<parameter name="Suffix">filtered</parameter>
<parameter name="Remove original mass list">false</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.masslistmethods.ADAPchromatogrambuilder.ADAPChromatogramBuilderModule">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Scans">
<ms_level>1</ms_level>
</parameter>
<parameter name="Mass list">masses filtered</parameter>
<parameter name="Min group size in # of scans">3</parameter>
<parameter name="Group intensity threshold">0.0</parameter>
<parameter name="Min highest intensity">0.0</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>0.0015</absolutetolerance>
<ppmtolerance>15.0</ppmtolerance>
</parameter>
<parameter name="Suffix">chromatograms</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.filtering.groupms2.GroupMS2Module">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Retention time tolerance" type="percent">1.0</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>0.4</absolutetolerance>
<ppmtolerance>5.0</ppmtolerance>
</parameter>
<parameter name="Limit by RT edges">false</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.identification.spectraldbsearch.LocalSpectralDBSearchModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="MassList">masses filtered</parameter>
<parameter name="Database file">
<current_file>D:\git\tattoo_pigments_spectral_libraries\20190730_timstof_pos_MS2.json</current_file>
<last_file>D:\git\tattoo_pigments_spectral_libraries\20190730_timstof_pos_MS2.json</last_file>
</parameter>
<parameter name="MS level">2</parameter>
<parameter name="Precursor m/z tolerance">
<absolutetolerance>0.05</absolutetolerance>
<ppmtolerance>20.0</ppmtolerance>
</parameter>
<parameter name="Minimum ion intensity">0.0</parameter>
<parameter name="13C deisotoping" selected="false">
<parameter name="m/z tolerance">
<absolutetolerance>0.001</absolutetolerance>
<ppmtolerance>5.0</ppmtolerance>
</parameter>
<parameter name="Monotonic shape"/>
<parameter name="Maximum charge"/>
</parameter>
<parameter name="Crop spectra to m/z overlap">true</parameter>
<parameter name="Spectral m/z tolerance">
<absolutetolerance>0.002</absolutetolerance>
<ppmtolerance>30.0</ppmtolerance>
</parameter>
<parameter name="Retention time tolerance" selected="false"/>
<parameter name="Minimum matched signals">2</parameter>
<parameter name="Similarity" selected="Weighted dot-product cosine">
<module name="Weighted dot-product cosine">
<parameter name="Weights">MassBank (mz^2 * I^0.5)</parameter>
<parameter name="Minimum cos similarity">0.15</parameter>
<parameter name="Remove unmatched signals">false</parameter>
</module>
<module name="Composite dot -product identity (similar to NIST search)">
<parameter name="Weights">MassBank (mz^2 * I^0.5)</parameter>
<parameter name="Minimum cos similarity">0.7</parameter>
</module>
</parameter>
</batchstep>
</batch>
<?xml version="1.0" encoding="UTF-8"?>
<batch>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesModule">
<parameter name="Raw data files" type="ALL_FILES"/>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.merge.RawFileMergeModule">
<parameter name="Raw data files" type="ALL_FILES"/>
<parameter name="Mode">MERGE SELECTED</parameter>
<parameter name="Grouping identifier position">AFTER LAST</parameter>
<parameter name="Position marker">_</parameter>
<parameter name="MS2 marker" selected="false"/>
<parameter name="Suffix to new name">_merged</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.filtering.scanfilters.ScanFiltersModule">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Scans"/>
<parameter name="Suffix">filtered</parameter>
<parameter name="Filter" selected="Savitzky-Golay filter">
<module name="Savitzky-Golay filter">
<parameter name="Number of datapoints">9</parameter>
</module>
<module name="Mean filter">
<parameter name="Window length"/>
</module>
<module name="Resampling filter">
<parameter name="m/z bin length"/>
</module>
<module name="Round resampling filter">
<parameter name="Sum duplicate intensities">false</parameter>
<parameter name="Remove zero intensity m/z peaks">true</parameter>
</module>
</parameter>
<parameter name="Remove source file after filtering">false</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Scans">
<ms_level>1</ms_level>
<scan_definition/>
</parameter>
<parameter name="Mass detector" selected="Exact mass">
<module name="Centroid">
<parameter name="Noise level">100.0</parameter>
</module>
<module name="Exact mass">
<parameter name="Noise level">300.0</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>
</parameter>
<parameter name="Mass list name">masses</parameter>
<parameter name="Output netCDF filename (optional)" selected="false"/>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Scans">
<ms_level>2</ms_level>
<scan_definition/>
</parameter>
<parameter name="Mass detector" selected="Exact mass">
<module name="Centroid">
<parameter name="Noise level">100.0</parameter>
</module>
<module name="Exact mass">
<parameter name="Noise level">120.0</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>
</parameter>
<parameter name="Mass list name">masses</parameter>
<parameter name="Output netCDF filename (optional)" selected="false"/>
</batchstep>
<batchstep method="net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterModule">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Mass list">masses</parameter>
<parameter name="Mass resolution">15000.0</parameter>
<parameter name="Peak model function">Lorentzian</parameter>
<parameter name="Suffix">filtered</parameter>
<parameter name="Remove original mass list">false</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.masslistmethods.ADAPchromatogrambuilder.ADAPChromatogramBuilderModule">
<parameter name="Raw data files" type="BATCH_LAST_FILES"/>
<parameter name="Scans">
<ms_level>1</ms_level>
</parameter>
<parameter name="Mass list">masses filtered</parameter>
<parameter name="Min group size in # of scans">3</parameter>
<parameter name="Group intensity threshold">0.0</parameter>
<parameter name="Min highest intensity">0.0</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>0.0015</absolutetolerance>
<ppmtolerance>15.0</ppmtolerance>
</parameter>
<parameter name="Suffix">chromatograms</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.filtering.groupms2.GroupMS2Module">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="Retention time tolerance" type="percent">1.0</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>0.4</absolutetolerance>
<ppmtolerance>5.0</ppmtolerance>
</parameter>
<parameter name="Limit by RT edges">false</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.peaklistmethods.identification.spectraldbsearch.LocalSpectralDBSearchModule">
<parameter name="Peak lists" type="BATCH_LAST_PEAKLISTS"/>
<parameter name="MassList">masses filtered</parameter>
<parameter name="Database file">
<current_file>D:\git\tattoo_pigments_spectral_libraries\20190730_timstof_pos_MS2.json</current_file>
<last_file>D:\git\tattoo_pigments_spectral_libraries\20190730_timstof_pos_MS2.json</last_file>
</parameter>
<parameter name="MS level">2</parameter>
<parameter name="Precursor m/z tolerance">
<absolutetolerance>0.05</absolutetolerance>
<ppmtolerance>20.0</ppmtolerance>
</parameter>
<parameter name="Minimum ion intensity">0.0</parameter>
<parameter name="13C deisotoping" selected="false">
<parameter name="m/z tolerance">
<absolutetolerance>0.001</absolutetolerance>
<ppmtolerance>5.0</ppmtolerance>
</parameter>
<parameter name="Monotonic shape"/>
<parameter name="Maximum charge"/>
</parameter>
<parameter name="Crop spectra to m/z overlap">true</parameter>
<parameter name="Spectral m/z tolerance">
<absolutetolerance>0.002</absolutetolerance>
<ppmtolerance>30.0</ppmtolerance>
</parameter>
<parameter name="Retention time tolerance" selected="false"/>
<parameter name="Minimum matched signals">2</parameter>
<parameter name="Similarity" selected="Weighted dot-product cosine">
<module name="Weighted dot-product cosine">
<parameter name="Weights">MassBank (mz^2 * I^0.5)</parameter>
<parameter name="Minimum cos similarity">0.15</parameter>
<parameter name="Remove unmatched signals">false</parameter>
</module>
<module name="Composite dot -product identity (similar to NIST search)">
<parameter name="Weights">MassBank (mz^2 * I^0.5)</parameter>
<parameter name="Minimum cos similarity">0.7</parameter>
</module>
</parameter>
</batchstep>
</batch>
0 ..._batch_full_peaklist+precursor_search.xml → ..._batch_full_peaklist+precursor_search.xml
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