GlycoWorkBench file reading problem

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august
Phosphoserine Member
Phosphoserine Member
Posts: 12
Joined: Tue Jan 07, 2014 8:59 am

GlycoWorkBench file reading problem

Postby august » Tue Jul 25, 2017 8:10 am

We have some MS1 files of some rleased glycans from by a Thermo QEXACTIVE machine. I wish to run GlycoWorkBench on them to characterize the Glycans. However having some issues when GlycoWorkBench is trying to read the files.

I first converted the RAW files to mzXML using MSCONVERT using the PeakPicking filter(as its MS1, mgf files cant be made out of RAW ) and tried GWB to read it. However it issued the following error when trying to read the mzXML file

Can anyone help to troubleshoot the problem?


Thanks in advance

Code: Select all

java.lang.RuntimeException: Can't file a reader for C:\Users\XYZ\Documents\ABC\TEST_GLYCAN_RAW\PEAK_PICKED\IgG_GlycanpH.mzXML
   at org.proteomecommons.io.xml.GenericXMLPeakListReaderFactory.newInstance(GenericXMLPeakListReaderFactory.java:97)
   at org.proteomecommons.io.GenericPeakListReader.getPeakListReader(GenericPeakListReader.java:176)
   at org.eurocarbdb.application.glycoworkbench.SpectraDocument.readSpectra(SpectraDocument.java:159)
   at org.eurocarbdb.application.glycoworkbench.SpectraDocument.open(SpectraDocument.java:98)
   at org.eurocarbdb.application.glycoworkbench.GlycoWorkbench.onOpen(GlycoWorkbench.java:3078)
   at org.eurocarbdb.application.glycoworkbench.GlycoWorkbench.onOpen(GlycoWorkbench.java:2965)
   at org.eurocarbdb.application.glycoworkbench.plugin.SpectraPanel.actionPerformed(SpectraPanel.java:987)
   at org.eurocarbdb.application.glycanbuilder.GlycanAction.actionPerformed(GlycanAction.java:227)
   at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
   at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
   at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
   at org.pushingpixels.substance.internal.utils.RolloverButtonListener.mouseReleased(RolloverButtonListener.java:124)
   at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
   at java.awt.Component.processMouseEvent(Unknown Source)
   at javax.swing.JComponent.processMouseEvent(Unknown Source)
   at java.awt.Component.processEvent(Unknown Source)
   at java.awt.Container.processEvent(Unknown Source)
   at java.awt.Component.dispatchEventImpl(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Window.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
   at java.awt.EventQueue.access$500(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
   at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue.dispatchEvent(Unknown Source)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.run(Unknown Source)

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