Support for MS3-based quantification

[dblyon]

Hi reporter-team,

I'm encountering an error when processing PeptideShaker results. I've attached the bug report, I'd gladly share the PeptideShaker reults, but they are too big (even when compressed) to attach them here. I can send them via e.g. wetransfer.
Reporter 0.9.7 log.txt
Your help would be much appreciated!!

Best regards,
David

[dblyon]

sent the file via wetransfer.

[dblyon]

javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31)
at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
at eu.isas.reporter.gui.ReporterGUI.checkForNewVersion(ReporterGUI.java:1560)
at eu.isas.reporter.gui.ReporterGUI.(ReporterGUI.java:219)
at eu.isas.reporter.gui.ReporterGUI.main(ReporterGUI.java:1313)
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31)
at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
at eu.isas.reporter.gui.ReporterGUI.checkForNewVersion(ReporterGUI.java:1560)
at eu.isas.reporter.gui.ReporterGUI.(ReporterGUI.java:219)
at eu.isas.reporter.gui.ReporterGUI.main(ReporterGUI.java:1313)
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31)
at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
at eu.isas.reporter.gui.ReporterGUI.checkForNewVersion(ReporterGUI.java:1560)
at eu.isas.reporter.gui.ReporterGUI.(ReporterGUI.java:219)
at eu.isas.reporter.gui.ReporterGUI.main(ReporterGUI.java:1313)
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31)
at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
at eu.isas.reporter.gui.ReporterGUI.checkForNewVersion(ReporterGUI.java:1560)
at eu.isas.reporter.gui.ReporterGUI.(ReporterGUI.java:219)
at eu.isas.reporter.gui.ReporterGUI.main(ReporterGUI.java:1313)
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31)
at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
at eu.isas.reporter.gui.ReporterGUI.checkForNewVersion(ReporterGUI.java:1560)
at eu.isas.reporter.gui.ReporterGUI.(ReporterGUI.java:219)
at eu.isas.reporter.gui.ReporterGUI.main(ReporterGUI.java:1313)
java.lang.ArrayIndexOutOfBoundsException: -1
at java.util.ArrayList.elementData(Unknown Source)
at java.util.ArrayList.get(Unknown Source)
at eu.isas.reporter.gui.resultpanels.OverviewPanel.displayClusters(OverviewPanel.java:379)
at eu.isas.reporter.gui.resultpanels.OverviewPanel.access$400(OverviewPanel.java:75)
at eu.isas.reporter.gui.resultpanels.OverviewPanel$2.run(OverviewPanel.java:289)
java.lang.NullPointerException
at com.compomics.util.gui.error_handlers.HelpDialog.(HelpDialog.java:91)
at com.compomics.util.gui.error_handlers.HelpDialog.(HelpDialog.java:69)
at eu.isas.reporter.gui.resultpanels.OverviewPanel.ratioPlotHelpJButtonActionPerformed(OverviewPanel.java:1768)
at eu.isas.reporter.gui.resultpanels.OverviewPanel.access$3000(OverviewPanel.java:75)
at eu.isas.reporter.gui.resultpanels.OverviewPanel$13.actionPerformed(OverviewPanel.java:1116)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$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 java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
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)
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31)
at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
at eu.isas.reporter.gui.ReporterGUI.checkForNewVersion(ReporterGUI.java:1560)
at eu.isas.reporter.gui.ReporterGUI.(ReporterGUI.java:219)
at eu.isas.reporter.gui.ReporterGUI.main(ReporterGUI.java:1313)
java.lang.UnsupportedOperationException: Normalization method not implemented.
at eu.isas.reporter.calculation.normalization.Normalizer.setPeptideNormalizationFactors(Normalizer.java:430)
at eu.isas.reporter.gui.ReporterGUI.displayResults(ReporterGUI.java:440)
at eu.isas.reporter.gui.ReporterGUI.access$100(ReporterGUI.java:81)
at eu.isas.reporter.gui.ReporterGUI$2.run(ReporterGUI.java:365)
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31)
at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
at eu.isas.reporter.gui.ReporterGUI.checkForNewVersion(ReporterGUI.java:1560)
at eu.isas.reporter.gui.ReporterGUI.(ReporterGUI.java:219)
at eu.isas.reporter.gui.ReporterGUI.main(ReporterGUI.java:1313)
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31)
at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
at eu.isas.reporter.gui.ReporterGUI.checkForNewVersion(ReporterGUI.java:1560)
at eu.isas.reporter.gui.ReporterGUI.(ReporterGUI.java:219)
at eu.isas.reporter.gui.ReporterGUI.main(ReporterGUI.java:1313)
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31)
at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
at eu.isas.reporter.gui.ReporterGUI.checkForNewVersion(ReporterGUI.java:1560)
at eu.isas.reporter.gui.ReporterGUI.(ReporterGUI.java:219)
at eu.isas.reporter.gui.ReporterGUI.main(ReporterGUI.java:1313)
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(Unknown Source)
at com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(Unknown Source)
at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31)
at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
at eu.isas.reporter.gui.ReporterGUI.checkForNewVersion(ReporterGUI.java:1560)
at eu.isas.reporter.gui.ReporterGUI.(ReporterGUI.java:219)
at eu.isas.reporter.gui.ReporterGUI.main(ReporterGUI.java:1313)
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50]
Message: White spaces are required between publicId and systemId.
at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652)
at java.xml/com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(XMLEventReaderImpl.java:83)
at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31)
at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37)
at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522)
at eu.isas.reporter.gui.ReporterGUI.checkForNewVersion(ReporterGUI.java:1560)
at eu.isas.reporter.gui.ReporterGUI.(ReporterGUI.java:219)
at eu.isas.reporter.gui.ReporterGUI.main(ReporterGUI.java:1313)
java.lang.IndexOutOfBoundsException: Index -1 out of bounds for length 12
at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:100)
at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:106)
at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:302)
at java.base/java.util.Objects.checkIndex(Objects.java:359)
at java.base/java.util.ArrayList.get(ArrayList.java:427)
at eu.isas.reporter.gui.resultpanels.OverviewPanel.displayClusters(OverviewPanel.java:379)
at eu.isas.reporter.gui.resultpanels.OverviewPanel.access$400(OverviewPanel.java:75)
at eu.isas.reporter.gui.resultpanels.OverviewPanel$2.run(OverviewPanel.java:289)

[hbarsnes]

Hi David,

Thanks for letting us know about this issue.

Most of the error messages seem to be related to the check for new versions. I will look into it, but these can safely be ignored.

For the real error I would need your data, but were did you send the wetransfer link? As I cannot seem to find it? Perhaps you can send it to me at harald.barsnes@gmail.com?

Best regards,
Harald

[dblyon]

Hi Harald, Thank you for the quick reply and specially for looking into this! This link should work: https://we.tl/t-mS0kq0YoUW?src=dnl <https://we.tl/t-mS0kq0YoUW?src=dnl> Best, David

…

On Tue, Jun 7, 2022, 23:58 Harald Barsnes ***@***.***> wrote: Hi David, Thanks for letting us know about this issue. Most of the error messages seem to be related to the check for new versions. I will look into it, but these can safely be ignored. For the real error I would need your data, but were did you send the wetransfer link? As I cannot seem to find it? Perhaps you can send it to me at ***@***.***? Best regards, Harald — Reply to this email directly, view it on GitHub <#22 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQH35F4PL2UJSLQLFKXO63VN7AX7ANCNFSM5X64ETKA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[hbarsnes]

Hi again,

The check for new versions has now been fixed and a new release is available: https://genesis.ugent.be/maven2/eu/isas/reporter/Reporter/0.9.8/Reporter-0.9.8.zip

Thanks for sharing the PeptideShaker project. However, to reproduce the error I will also need the FASTA and spectrum files. The easiest option is to use "Export > PeptideShaker Project As > Zip File" when having the project open in PeptideShaker.

Could you also make sure that you are using the latest versions of both PeptideShaker and Reporter? As there are definitely some versions of the two tools that are not compatible with each other.

Best regards,
Harald

[dblyon]

Good morning Harald, Thanks for the link and the quick feedback ! I've downloaded the latest build of Reporter and tried re-running Reporter. As you anticipated it crashed with the following error message:

jshortcut.dll loaded via tmp generated pathname: C:\Users\SA_MRT~1\AppData\Local\Temp\2\jshortcut-1001257037006933067.dll java.lang.IndexOutOfBoundsException: Index -1 out of bounds for length 12 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:100) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:106) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:302) at java.base/java.util.Objects.checkIndex(Objects.java:359) at java.base/java.util.ArrayList.get(ArrayList.java:427) at eu.isas.reporter.gui.resultpanels.OverviewPanel.displayClusters(OverviewPanel.java:379) at eu.isas.reporter.gui.resultpanels.OverviewPanel.access$400(OverviewPanel.java:75) at eu.isas.reporter.gui.resultpanels.OverviewPanel$2.run(OverviewPanel.java:289)

*Version numbers* of programs used (they are the latest versions as far as I know, comparing to what's stated here: http://compomics.github.io/projects ) * SearchGUI-4.1.11 * Peptide Shaker 2.2.8 * Reporter-0.9.7 --> Reporter-0.9.8 Please find *the files* I've used for processing here: https://monterosatx.egnyte.com/fl/JljRUjGEXS Password: YCE3f2NSRqYN Thank you very much for your support !! Best, David

…

On Wed, Jun 8, 2022 at 12:46 AM Harald Barsnes ***@***.***> wrote: Hi again, The check for new versions has now been fixed and a new release is available: https://genesis.ugent.be/maven2/eu/isas/reporter/Reporter/0.9.8/Reporter-0.9.8.zip Thanks for sharing the PeptideShaker project. However, to reproduce the error I will also need the FASTA and spectrum files. The easiest option is to use "Export > PeptideShaker Project As > Zip File" when having the project open in PeptideShaker. Could you also make sure that you are using the latest versions of both PeptideShaker and Reporter? As there are definitely some versions of the two tools that are not compatible with each other. Best regards, Harald — Reply to this email directly, view it on GitHub <#22 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQH35G7ZDPPUOUI6Z5OHBTVN7GOBANCNFSM5X64ETKA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[hbarsnes]

Hi David,

Thanks for sharing the rest of the data. I can confirm that I now have all I need to reproduce the error. I will look into it as soon as I get the chance and get back to you.

Best regards,
Harald

[hbarsnes]

Hi again,

Seems like I was wrong when stating that I had everything I needed to reproduce the error, as I did not consider that you could have custom PTMs.

Could you please also send me the file called modificationFactory-X.Y.Z.json found in your "user_home".compomics folder? It contains the details of the user-defined PTMs.

Also, which Reporter Method are you using and which sample(s) do you select as the reference channel(s)?

Best regards,
Harald

[hbarsnes]

Could you please also send me the file called modificationFactory-X.Y.Z.json found in your "user_home".compomics folder?

Most likely the most recent version will be modificationFactory-5.0.1.json.

[dblyon]

Hi Harald,

Sorry about that. I wasn't aware these parameters weren't included.

I've attached the modificationFactory-5.0.1.json, but had to change the file extension to txt in order to upload it here on github.
modificationFactory-5.0.1.txt

Thank you for your help!

Best,
David

[dblyon]

PS: I've used the default settings from Reporter for quantification.

[hbarsnes]

Hi David,

I've had a closer look at your data and noticed that none of your spectra seem have any TMT reporter ions? You can check this by zooming in on the 126 to 135 range of your spectra. There should be report ions there but does not seem to be any? Which is strange given that most (if not all) of your peptides are labeled with TMT tags. Any idea why this would be the case? Perhaps the mass spectrometer was not set up correctly for TMT?

In any case, this could explain why Reporter is struggling and throwing the exception above. I can try to dig deeper into that error later, but probably worth figuring out the missing TMT reporter ions issue first, as without these there is not much for Reporter to quantify on...

Best regards,
Harald

[dblyon]

Hi Harald,

The MS2 level is used for identification only (CID fragmentation). We're quantifying using the MS3 level (using HCD fragmentation and SPS (Synchronous Precursor Selection)). So in MS2 in the low m/z region (< 200 m/z) you will not find the reporter ions, but you should find them in the MS3 level. The MS2 level fragmentation is run in a way that is "too soft" to produce nice reporter ion signals. The MS3 level is run in way that produces good reporter ion signals (and is used only for quant).
I hope this helps/makes sense.

Best,
David