Dear Mzmine developers,
Thank you so much for developing this wonderful tool! I think I found a bug
in the newest 2.11 release. I was trying to do targeted peak picking for my
files acquired on an Agilent QTOF. The .d files were converted to mzXML
files by msconvert, and were imported into Mzmine 2.11. Then I did targeted
peak picking with the following parameters:
Intensity tolerance: 50%
m/z tolerance: 0.0025 m/z or 10 ppm
Retention time tolerance 0.35 absolute min
The peak height values were fine, but the peak area values were all
negative and way too big. I then used Mzmine 2.9 to do the same analysis
and the peak area values were good. I have attached the screen shots of
both analysis and the log message in Mzmine 2.11. I think there is a bug in
the targeted peak picking module in the 2.11 version.
I am using 64-bit Windows 7 operating system. The R version is 2.15.1. All
the R packages are up-to-date. I did not change the HEAP_SIZE setting in
the startMZmine script. Please let me know if you need more information.
Thank you!
Grace
java version "1.6.0_25"
Java(TM) SE Runtime Environment (build 1.6.0_25-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.0-b11, mixed mode)
[13:13:55|INFO|MZmineCore]: Starting MZmine 2.11
[13:13:55|FINE|TmpFileCleanup]: Checking for old temporary files...
[13:13:55|FINE|MZmineCore]: Loading core classes..
[13:13:55|FINE|MZmineCore]: Initializing core classes..
[13:13:55|FINE|MZmineCore]: Loading modules
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethod
s.projectload.ProjectLoadModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethod
s.projectsave.ProjectSaveModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethod
s.projectsave.ProjectSaveAsModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethod
s.projectclose.ProjectCloseModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.batchmode.Bat
chModeModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.rawdataimport.RawDataImportModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.peakpicking.massdetection.MassDetectionModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.masslistmetho
ds.shoulderpeaksfilter.ShoulderPeaksFilterModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.masslistmetho
ds.chromatogrambuilder.ChromatogramBuilderModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.peakpicking.gridmass.GridMassModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.peakpicking.manual.ManualPeakPickerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.peakpicking.msms.MsMsPeakPickerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.filtering.scanfilters.ScanFiltersModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.filtering.datasetfilters.DataSetFiltersModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.filtering.baselinecorrection.BaselineCorrectionModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.filtering.alignscans.AlignScansModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.filtering.scansmoothing.ScanSmoothingModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.alignment.join.JoinAlignerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.alignment.ransac.RansacAlignerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.csvexport.CSVExportModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.xmlexport.XMLExportModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.xmlimport.XMLImportModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.sqlexport.SQLExportModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.gapfilling.peakfinder.PeakFinderModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.gapfilling.samerange.SameRangeGapFillerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.isotopes.deisotoper.IsotopeGrouperModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.isotopes.isotopeprediction.IsotopePatternCalculator
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.peakpicking.smoothing.SmoothingModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.peakpicking.deconvolution.DeconvolutionModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.peakpicking.shapemodeler.ShapeModelerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.peakpicking.peakextender.PeakExtenderModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.targetedpeakdetection.TargetedPeakDetectionModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.filtering.duplicatefilter.DuplicateFilterModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.filtering.rowsfilter.RowsFilterModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.normalization.rtnormalizer.RTNormalizerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.normalization.linear.LinearNormalizerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.normalization.standardcompound.StandardCompoundNormalizerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.rtmzplots.cvplot.CVPlotModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.rtmzplots.logratioplot.LogratioPlotModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.projectionplots.PCAPlotModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.projectionplots.CDAPlotModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.projectionplots.SammonsPlotModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.clustering.ClusteringModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.heatmaps.HeatMapModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.custom.CustomDBSearchModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.formulaprediction.FormulaPredictionModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.fragmentsearch.FragmentSearchModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.adductsearch.AdductSearchModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.complexsearch.ComplexSearchModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.dbsearch.OnlineDBSearchModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.glycerophospholipidsearch.GPLipidSearchModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.camera.CameraSearchModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.nist.NistMsSearchModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.formulapredictionpeaklist.FormulaPredictionPeakListModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.tic.TICVisualizerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.spectra.SpectraVisualizerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.twod.TwoDVisualizerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.threed.ThreeDVisualizerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.neutralloss.NeutralLossVisualizerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.peaklist.PeakListTableModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.peaklist.export.IsotopePatternExportModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.peaklist.export.MSMSExportModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.scatterplot.ScatterPlotVisualizerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.histogram.HistogramVisualizerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.infovisualizer.InfoVisualizerModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.intensityplot.IntensityPlotModule
[13:13:55|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.tools.mzrange
calculator.MzRangeCalculatorModule
[13:13:55|FINE|MZmineCore]: Initializing GUI
[13:13:56|FINEST|MZmineConfigurationImpl]: Loading desktop configuration
[13:13:56|FINEST|MZmineConfigurationImpl]: Loading modules configuration
[13:13:56|INFO|MZmineConfigurationImpl]: Loaded configuration from file conf\con
fig.xml
[13:13:56|INFO|MZmineCore]: Showing main window
[13:13:58|FINEST|MainMenu]: Setting parameters for module Raw data import
[13:14:00|FINEST|MainMenu]: Starting module Raw data import with parameters Raw
data file names: [F:\GraceYang\metabolomics\data\Hilic\20140603_Hilic_Amide_ESI_
neg_HeteroSamples\mzXML\Hilic_23_nc_1.mzXML]
[13:14:00|FINEST|TaskQueue]: Adding task "Opening fileF:\GraceYang\metabolomics\
data\Hilic\20140603_Hilic_Amide_ESI_neg_HeteroSamples\mzXML\Hilic_23_nc_1.mzXML"
to the task controller queue
[13:14:00|FINEST|WorkerThread]: Starting processing of task: Opening fileF:\Grac
eYang\metabolomics\data\Hilic\20140603_Hilic_Amide_ESI_neg_HeteroSamples\mzXML\H
ilic_23_nc_1.mzXML
[13:14:00|INFO|MzXMLReadTask]: Started parsing file F:\GraceYang\metabolomics\da
ta\Hilic\20140603_Hilic_Amide_ESI_neg_HeteroSamples\mzXML\Hilic_23_nc_1.mzXML
[13:14:01|FINEST|RawDataFileImpl]: Writing of scans to file C:\Users\GRACEY~1\Ap
pData\Local\Temp\mzmine8020155445604144732.scans finished
[13:14:01|INFO|MzXMLReadTask]: Finished parsing F:\GraceYang\metabolomics\data\H
ilic\20140603_Hilic_Amide_ESI_neg_HeteroSamples\mzXML\Hilic_23_nc_1.mzXML, parse
d 1062 scans
[13:14:05|FINEST|MainMenu]: Setting parameters for module Targeted peak detectio
n
[13:14:07|FINEST|MainMenu]: Starting module Targeted peak detection with paramet
ers Raw data files: [Hilic_23_nc_1.mzXML], Name suffix: detectedPeak, Peak list
file: F:\GraceYang\metabolomics\Negative Masses.csv, Field separator: ,, Ignore
first line: true, Intensity tolerance: 0.5, m/z tolerance: 0.0025 m/z or 10.0 pp
m, Retention time tolerance: 0.35 min
[13:14:07|FINEST|TaskQueue]: Adding task "Targeted peak detection Hilic_23_nc_1.
mzXML" to the task controller queue
[13:14:07|FINEST|WorkerThread]: Starting processing of task: Targeted peak detec
tion Hilic_23_nc_1.mzXML
[13:14:07|INFO|TargetedPeakDetectionModuleTask]: Targeted peak detection on {0}
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