Error: Feature "1" has more than one MSLEVEL=1 record

[Brian Sedio]

Hello Team,

I am running MZmine 3 for FBMN (and IIMN) networking, and annotation using Sirius. I am running Sirius and Qemistree on the Frontera superocmputer, as follows:

singularity exec $SCRATCH/sediob_qiime2_2021_8.sif qiime qemistree compute-fragmentation-trees --p-sirius-path '/scratch1/06619/sediob/Sirius4.9.9/sirius/bin'
--i-features /scratch1/06619/sediob/ChemEcol/coleman_4e4_mzm3_20221021_sirius.mgf.qza
--p-ppm-max 15
--p-profile orbitrap
--p-ions-considered '[M+H]+'
--p-java-flags "-Djava.io.tmpdir=/scratch1/06619/sediob/ChemEcol/QemistreeTemp/ -Xms900G -Xmx1600G"
--o-fragmentation-trees /scratch1/06619/sediob/ChemEcol/coleman_4e4_mzm3_20221021_fragmentation_trees.qza

This "compute-fragmentation-trees" command results in the following error:

Feature "1" has more than one MSLEVEL=1 record

I have never received this error when using MZmine 2, but haven't been able to avoid it while using MZmine 3. Is there some grouping step that is bundling MS1 records while combining features that may be confusing Sirius?

Below is an example of an MZmine 3 .xml batch file, that generated a _sirius.mgf file that resulting in the above error.

Thank you very much for any feedback,
Brian

<batchstep method="io.github.mzmine.modules.io.import_rawdata_all.AllSpectralDataImportModule"> <parameter name="File names"> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff001.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff002.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff003.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff004.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff005.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff006.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff007.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff008.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff009.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff010.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff011.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff012.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff013.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff014.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff015.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff016.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff017.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff018.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff019.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff020.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff021.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff022.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff023.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff024.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff025.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff026.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff027.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff028.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff029.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff030.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff031.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff032.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff033.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff034.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff035.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff036.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff037.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff038.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff039.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff040.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff041.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff042.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff043.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff044.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff045.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff046.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff047.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff048.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff049.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff050.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff051.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff052.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff053.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff054.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff055.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff056.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff057.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff058.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff059.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff060.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff061.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff062.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff063.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff064.mzXML</file> <file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/Coleman_Jeff-selected/Jeff065.mzXML</file> </parameter> <parameter name="Advanced import" selected="false"> <parameter name="MS1 detector (Advanced)" selected="false" selected_item="Factor of lowest signal"> <module name="Factor of lowest signal"> <parameter name="Noise factor">2.5</parameter> </module> <module name="Centroid"> <parameter name="Noise level">0.0</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> 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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="MS2 detector (Advanced)" selected="false" selected_item="Factor of lowest signal"> <module name="Factor of lowest signal"> <parameter name="Noise factor">2.5</parameter> </module> <module name="Centroid"> <parameter name="Noise level">0.0</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> <module name="Exact mass"> <parameter name="Noise level"/> <parameter name="Detect isotope signals below noise level" selected="false"> <parameter name="Chemical 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m/z">1</parameter> </parameter> </module> </parameter> </parameter> <parameter name="Spectral library files"/> </batchstep> <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_massdetection.MassDetectionModule"> <parameter name="Raw data files" type="BATCH_LAST_FILES"/> <parameter name="Scans"> <ms_level>1</ms_level> </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">40000.0</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> <module 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name="m/z tolerance"> <absolutetolerance>0.001</absolutetolerance> <ppmtolerance>5.0</ppmtolerance> </parameter> <parameter name="Maximum charge of isotope m/z">2</parameter> </parameter> </module> </parameter> <parameter name="Output netCDF filename (optional)" selected="true"> <current_file>/</current_file> <last_file>/</last_file> </parameter> </batchstep> <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_massdetection.MassDetectionModule"> <parameter name="Raw data files" type="BATCH_LAST_FILES"/> <parameter name="Scans"> <ms_level>2</ms_level> </parameter> <parameter name="Scan types (IMS)">All scan types</parameter> <parameter name="Mass detector" selected_item="Auto"> <module name="Factor of lowest signal"> <parameter name="Noise factor">2.5</parameter> </module> <module name="Centroid"> <parameter name="Noise level">0.0</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> <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">0.0</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>0.001</absolutetolerance> <ppmtolerance>5.0</ppmtolerance> </parameter> <parameter name="Maximum charge of isotope m/z">2</parameter> </parameter> </module> </parameter> <parameter name="Output netCDF filename (optional)" selected="true"> <current_file>/</current_file> <last_file>/</last_file> </parameter> </batchstep> <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_adapchromatogrambuilder.ModularADAPChromatogramBuilderModule"> <parameter name="Raw data files" type="BATCH_LAST_FILES"/> <parameter name="Scans"> <retention_time> <min>0.0</min> <max>20.0</max> </retention_time> <ms_level>1</ms_level> </parameter> <parameter name="Min group size in # of scans">4</parameter> <parameter name="Group intensity threshold">50000.0</parameter> <parameter name="Min highest intensity">100000.0</parameter> <parameter name="Scan to scan accuracy (m/z)"> <absolutetolerance>0.001</absolutetolerance> <ppmtolerance>5.0</ppmtolerance> </parameter> <parameter name="Suffix">chroms</parameter> <parameter name="Allow single scan chromatograms"/> </batchstep> <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_smoothing.SmoothingModule"> <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> <parameter name="Smoothing algorithm" selected_item="Savitzky Golay"> <module name="Savitzky Golay"> <parameter name="Retention time smoothing" selected="true">5</parameter> <parameter name="Mobility smoothing" selected="false">13</parameter> </module> <module name="Loess smoothing"> <parameter name="Retention time width (scans)" selected="false">5</parameter> <parameter name="Mobility width (scans)" selected="false">5</parameter> </module> </parameter> <parameter name="Original feature list">REMOVE</parameter> <parameter name="Suffix">sm</parameter> </batchstep> <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_chromatogramdeconvolution.minimumsearch.MinimumSearchFeatureResolverModule"> <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> <parameter name="Suffix">r</parameter> <parameter name="Original feature list">REMOVE</parameter> <parameter name="MS/MS scan pairing" selected="true"> <parameter name="Retention time tolerance" unit="MINUTES">0.90000004</parameter> <parameter name="MS1 to MS2 precursor tolerance (m/z)"> <absolutetolerance>0.001</absolutetolerance> <ppmtolerance>5.0</ppmtolerance> </parameter> <parameter name="Limit by RT edges">true</parameter> <parameter name="Combine MS/MS spectra (TIMS)">false</parameter> <parameter name="Lock to feature mobility range">true</parameter> <parameter name="Minimum merged intensity (IMS)" selected="false">0.0</parameter> </parameter> <parameter name="Dimension">Retention time</parameter> <parameter name="Chromatographic threshold">0.7</parameter> <parameter name="Minimum search range RT/Mobility (absolute)">0.30000001192092896</parameter> <parameter name="Minimum relative height">0.0</parameter> <parameter name="Minimum absolute height">100000.0</parameter> <parameter name="Min ratio of peak top/edge">1.8</parameter> <parameter name="Peak duration range (min/mobility)"> <min>0.0</min> <max>9.000000357627869</max> </parameter> <parameter name="Min # of data points">4</parameter> </batchstep> <batchstep method="io.github.mzmine.modules.dataprocessing.filter_isotopegrouper.IsotopeGrouperModule"> <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> <parameter name="Name suffix">deiso</parameter> <parameter name="m/z tolerance"> <absolutetolerance>0.001</absolutetolerance> <ppmtolerance>5.0</ppmtolerance> </parameter> <parameter name="Retention time tolerance" unit="MINUTES">0.1</parameter> <parameter name="Mobility tolerance" selected="false">0.008</parameter> <parameter name="Monotonic shape">true</parameter> <parameter name="Maximum charge">2</parameter> <parameter name="Representative isotope">Most intense</parameter> <parameter name="Never remove feature with MS2">true</parameter> <parameter name="Original feature list">REMOVE</parameter> </batchstep> <batchstep method="io.github.mzmine.modules.dataprocessing.filter_isotopefinder.IsotopeFinderModule"> <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> <parameter name="Chemical elements">H,C,N,O,S</parameter> <parameter name="m/z tolerance"> <absolutetolerance>0.001</absolutetolerance> <ppmtolerance>5.0</ppmtolerance> </parameter> <parameter name="Maximum charge of isotope m/z">1</parameter> <parameter name="Search in scans">SINGLE MOST INTENSE</parameter> </batchstep> <batchstep method="io.github.mzmine.modules.dataprocessing.align_join.JoinAlignerModule"> <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> <parameter name="Feature list name">Aligned feature list</parameter> <parameter name="m/z tolerance"> <absolutetolerance>0.001</absolutetolerance> <ppmtolerance>5.0</ppmtolerance> </parameter> <parameter name="Weight for m/z">3.0</parameter> <parameter name="Retention time tolerance" unit="MINUTES">0.2</parameter> <parameter name="Weight for RT">1.0</parameter> <parameter name="Mobility tolerance" selected="false">0.01</parameter> <parameter name="Mobility weight">1.0</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> <parameter name="Compare spectra similarity" selected="false"> <parameter name="Spectral m/z tolerance"> <absolutetolerance>0.001</absolutetolerance> <ppmtolerance>10.0</ppmtolerance> </parameter> <parameter name="MS level">2</parameter> <parameter name="Compare spectra similarity" selected_item="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">0.7</parameter> <parameter name="Handle unmatched signals">KEEP ALL AND MATCH TO ZERO</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> <parameter name="Handle unmatched signals">KEEP ALL AND MATCH TO ZERO</parameter> </module> </parameter> </parameter> <parameter name="Original feature list">REMOVE</parameter> </batchstep> <batchstep method="io.github.mzmine.modules.dataprocessing.filter_rowsfilter.RowsFilterModule"> <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> <parameter name="Name suffix">13C</parameter> <parameter name="Minimum features in a row (abs or %)" selected="false">1.0</parameter> <parameter name="Minimum features in an isotope pattern" selected="false">2</parameter> <parameter name="Validate 13C isotope pattern" selected="true"> <parameter name="m/z tolerance"> <absolutetolerance>0.001</absolutetolerance> <ppmtolerance>5.0</ppmtolerance> </parameter> <parameter name="Max charge">2</parameter> <parameter name="Estimate minimum carbon">true</parameter> <parameter name="Remove if 13C">true</parameter> <parameter name="Exclude isotopes">O</parameter> </parameter> <parameter name="m/z" selected="false"/> <parameter name="Retention time" selected="false"/> <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">true</parameter> <parameter name="Reset the feature number ID">false</parameter> <parameter name="Mass defect" selected="false"/> <parameter name="Original feature list">REMOVE</parameter> </batchstep> <batchstep method="io.github.mzmine.modules.io.export_features_gnps.fbmn.GnpsFbmnExportAndSubmitModule"> <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/> <parameter name="Filename"> <current_file>/Users/briansedio/Documents/GradStudents/Coleman_Jeffrey/coleman_4e4_mzm3_20221021_gnps</current_file> <last_file>/Users/briansedio/Documents/Bio384K_ChemicalEcology/Tutorial_2022/demo_carya_mzm3test3_20221004.mgf</last_file> <last_file>/Users/briansedio/Documents/Bio384K_ChemicalEcology/Tutorial_2022/demo_carya_mzm3test2_20221004.mgf</last_file> <last_file>/Users/briansedio/Documents/Bio384K_ChemicalEcology/Tutorial_2022/demo_carya_mzm3test_20221004.mgf</last_file> </parameter> <parameter name="Merge MS/MS (experimental)" selected="false"> <parameter name="Select spectra to merge">across samples</parameter> <parameter name="m/z merge mode">weighted average (remove outliers)</parameter> <parameter name="intensity merge mode">sum intensities</parameter> <parameter name="Expected mass deviation"> <absolutetolerance>0.0</absolutetolerance> <ppmtolerance>10.0</ppmtolerance> </parameter> <parameter name="Cosine threshold (%)">0.7</parameter> <parameter name="Signal count threshold (%)">0.2</parameter> <parameter name="Isolation window offset (m/z)">0.0</parameter> <parameter name="Isolation window width (m/z)">3.0</parameter> </parameter> <parameter name="Filter rows">MS2 OR ION IDENTITY</parameter> <parameter name="Feature intensity">Peak area</parameter> <parameter name="CSV export">SIMPLE</parameter> <parameter name="Submit to GNPS" selected="false"> <parameter name="Meta data file" selected="false"/> <parameter name="Export ion identity networks">true</parameter> <parameter name="Presets">HIGHRES</parameter> <parameter name="Job title"/> <parameter name="Email"/> <parameter name="Username"/> <parameter name="Password"/> <parameter name="Open website">true</parameter> </parameter> <parameter name="Open 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outliers)</parameter> <parameter name="intensity merge mode">sum intensities</parameter> <parameter name="Expected mass deviation"> <absolutetolerance>0.0</absolutetolerance> <ppmtolerance>10.0</ppmtolerance> </parameter> <parameter name="Cosine threshold (%)">0.7</parameter> <parameter name="Signal count threshold (%)">0.2</parameter> <parameter name="Isolation window offset (m/z)">0.0</parameter> <parameter name="Isolation window width (m/z)">3.0</parameter> </parameter> <parameter name="m/z tolerance"> <absolutetolerance>0.002</absolutetolerance> <ppmtolerance>5.0</ppmtolerance> </parameter> <parameter name="Renumber IDs">true</parameter> <parameter name="Only rows with annotation">false</parameter> <parameter name="Exclude empty MS/MS spectra">true</parameter> <parameter name="Exclude multiple charge">false</parameter> <parameter name="Exclude multimers">false</parameter> </batchstep>

[Helena Mannochio Russo]

Hi Brian,

Indeed, this is something that is happening with Mzmine3 sirius.mgf exports!

If you open the sirius.mgf file, you will see that there are, indeed, 'duplicated' MS1 spectra (for the same FEATURE_ID, there are two MSLEVEL=1). However, one of this duplicated MSLEVEL=1 is a SPECTYPE=CORRELATED MS. You can remove these SPECTYPE=CORRELATED MS (from the Begin Ions till the End Ions) from your sirius.mgf file, and Qemistree will work!

Best,

Helena Russo

[Brian Sedio]

Hi Helene,

Do you have a way to remove the SPECTYPE=CORRELATED MS from the sirius mgf file (other than manually)?

I wonder if we could write a regular expression in BBEdit/TextWrangler that could do it.

Thanks for your feedback,

Brian

[Helena Mannochio Russo]

Hi Brian,

Yes, I uploaded a Python script to my GitHub page: https://github.com/helenamrusso/Python_scripts .

You should just put as input your sirius.mgf file path and you will have the filtered one as output :)

I hope it helps!

I'll also update the documentation.

All the best,

Helena

[Brian Sedio]

Hi again Helena, everyone,

Here is a regular expression that can be used in BBEdit to identify and remove the spectra with SPECTYPE=CORRELATED:

(BEGIN IONS\rFEATURE_ID=\d\rPEPMASS=\d+.\d+\rCORR_GROUPID=\d\rCHARGE=\d\rRTINSECONDS=\d+.\d+\rSPECTYPE=CORRELATED MS\rMSLEVEL=1\rFILENAME=.+\r)(\d+.+\r){2,}(END IONS\r)

Put this regular expression in the "search" field and leave the "replace" field blank, and it should remove these spectra from the _sirius.mgf file and allow you to use Qemistree.

Thanks again Helena!

Brian