pride-toolsuite / pride-inspector Goto Github PK

Modifications in assay summary panel are displayed as accessions, this is less user friendly. It would be nice to have the proper name displayed.

We are still using some deprecated Java classes in Inspector, it would be nice to replace them with the more up-to-date ones.

PRIDE Inspector is unable to open or process a peak file which has a byte order mark (BOM) set in the file. This means the peak file cannot be visualised on its own, or added as a related spectra file for an mzIdentML file.

Thought I was going a bit crazy there for a while. Can be fixed by updating the input file to remove the BOM, but this isn't ideal.

The exception from the bottom right of Inspector:

Failed to retrieve spectrum related data
uk.ac.ebi.pride.utilities.data.controller.DataAccessException: Exception while trying to read Spectrum using Spectrum ID

And in the log file:

2015-03-25 12:07:12,162 ERROR [pool-2-thread-1] u.a.e.p.u.d.c.i.C.PeakControllerImpl [PeakControllerImpl.java:174] Get spectrum by id
uk.ac.ebi.pride.tools.jmzreader.JMzReaderException: MS2 query must start with 'BEGIN IONS'
at uk.ac.ebi.pride.tools.mgf_parser.model.Ms2Query.(Ms2Query.java:123) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.tools.mgf_parser.MgfFile.loadIndexedQueryFromFile(MgfFile.java:809) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.tools.mgf_parser.MgfFile.loadIndexedQueryFromFile(MgfFile.java:840) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.tools.mgf_parser.MgfFile.getMs2Query(MgfFile.java:779) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.tools.mgf_parser.MgfFile.getSpectrumById(MgfFile.java:1178) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.utilities.data.io.file.PeakUnmarshallerAdaptor.getSpectrumById(PeakUnmarshallerAdaptor.java:42) ~[ms-data-core-api-2.0.3.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl.getSpectrumById(PeakControllerImpl.java:168) ~[ms-data-core-api-2.0.3.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController.getSpectrumById(CachedDataAccessController.java:154) [ms-data-core-api-2.0.3.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController.getSpectrumMsLevel(AbstractDataAccessController.java:222) [ms-data-core-api-2.0.3.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController.getSpectrumMsLevel(CachedDataAccessController.java:268) [ms-data-core-api-2.0.3.jar:na]
at uk.ac.ebi.pride.toolsuite.gui.task.impl.RetrieveSpectrumTableTask.retrieve(RetrieveSpectrumTableTask.java:104) [pride-inspector-2.5.0.jar:na]
at uk.ac.ebi.pride.toolsuite.gui.task.impl.RetrieveSpectrumTableTask.retrieve(RetrieveSpectrumTableTask.java:25) [pride-inspector-2.5.0.jar:na]
at uk.ac.ebi.pride.toolsuite.gui.task.impl.AbstractDataAccessTask.doInBackground(AbstractDataAccessTask.java:47) [pride-inspector-2.5.0.jar:na]
at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_75]
at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_75]
at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_75]
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_75]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_75]
at java.lang.Thread.run(Unknown Source) [na:1.7.0_75]
2015-03-25 12:07:12,163 ERROR [pool-2-thread-1] u.a.e.p.t.g.t.i.RetrieveSpectrumTableTask [RetrieveSpectrumTableTask.java:132] Failed to retrieve spectrum related data
uk.ac.ebi.pride.utilities.data.controller.DataAccessException: Exception while trying to read Spectrum using Spectrum ID
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl.getSpectrumById(PeakControllerImpl.java:175) ~[ms-data-core-api-2.0.3.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController.getSpectrumById(CachedDataAccessController.java:154) ~[ms-data-core-api-2.0.3.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController.getSpectrumMsLevel(AbstractDataAccessController.java:222) ~[ms-data-core-api-2.0.3.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController.getSpectrumMsLevel(CachedDataAccessController.java:268) ~[ms-data-core-api-2.0.3.jar:na]
at uk.ac.ebi.pride.toolsuite.gui.task.impl.RetrieveSpectrumTableTask.retrieve(RetrieveSpectrumTableTask.java:104) [pride-inspector-2.5.0.jar:na]
at uk.ac.ebi.pride.toolsuite.gui.task.impl.RetrieveSpectrumTableTask.retrieve(RetrieveSpectrumTableTask.java:25) [pride-inspector-2.5.0.jar:na]
at uk.ac.ebi.pride.toolsuite.gui.task.impl.AbstractDataAccessTask.doInBackground(AbstractDataAccessTask.java:47) [pride-inspector-2.5.0.jar:na]
at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.7.0_75]
at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.7.0_75]
at javax.swing.SwingWorker.run(Unknown Source) [na:1.7.0_75]
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.7.0_75]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.7.0_75]
at java.lang.Thread.run(Unknown Source) [na:1.7.0_75]
Caused by: uk.ac.ebi.pride.tools.jmzreader.JMzReaderException: MS2 query must start with 'BEGIN IONS'
at uk.ac.ebi.pride.tools.mgf_parser.model.Ms2Query.(Ms2Query.java:123) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.tools.mgf_parser.MgfFile.loadIndexedQueryFromFile(MgfFile.java:809) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.tools.mgf_parser.MgfFile.loadIndexedQueryFromFile(MgfFile.java:840) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.tools.mgf_parser.MgfFile.getMs2Query(MgfFile.java:779) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.tools.mgf_parser.MgfFile.getSpectrumById(MgfFile.java:1178) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.utilities.data.io.file.PeakUnmarshallerAdaptor.getSpectrumById(PeakUnmarshallerAdaptor.java:42) ~[ms-data-core-api-2.0.3.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl.getSpectrumById(PeakControllerImpl.java:168) ~[ms-data-core-api-2.0.3.jar:na]
... 12 common frames omitted
at uk.ac.ebi.pride.tools.mgf_parser.MgfFile.getMs2Query(MgfFile.java:779) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.tools.mgf_parser.MgfFile.getSpectrumById(MgfFile.java:1178) ~[mgf-parser-1.2.9.jar:na]
at uk.ac.ebi.pride.utilities.data.io.file.PeakUnmarshallerAdaptor.getSpectrumById(PeakUnmarshallerAdaptor.java:42) ~[ms-data-core-api-2.0.3.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PeakControllerImpl.getSpectrumById(PeakControllerImpl.java:168) ~[ms-data-core-api-2.0.3.jar:na]
... 12 common frames omitted

The numeric bins of the intensity summary chart are fixed. The graph has too much whitespace when all of the distribution is in a couple of the bins. Chart Options should have the flexibility to specify the number of bins and their boundaries.

Charts about quantitation data Quality must be added.

Decoy protein and peptide hits only show numbers. It would be nice to also have a percentage. Additionally, it's unclear to me whether the number of target / decoy identifications also depends on the identification rank. Selecting a different rank to be displayed in the peptide view doesn't change anything.

just cloned the repo (master commit bf3dd55) and trying to build it. mvn install does not work

PS C:\Users\wolski\prog\pride-inspector> mvn -e install
[INFO] Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building pride-inspector 2.5.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[WARNING] The POM for uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for uk.ac.ebi.pride.tools:mzdata-parser:jar:1.2.2-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for uk.ac.ebi.pride.jaxb:pride-jaxb:jar:1.0.13-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for uk.ac.ebi.pride.utilities:pride-utilities:jar:2.0.5-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for uk.ac.ebi.pride.toolsuite:inspector-mzgraph-browser:jar:2.0.2-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for uk.ac.ebi.pride.toolsuite:inspector-quality-chart:jar:2.0.3-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for uk.ac.ebi.pride.toolsuite:inspector-swing-utils:jar:2.0.2-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for uk.ac.ebi.pride.utilities:pride-protein-inference:jar:0.0.5-SNAPSHOT is missing, no dependency information available
[WARNING] The POM for com.asperasoft:aspera-faspmanager:jar:2.7.0.42750 is missing, no dependency information available
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.850s
[INFO] Finished at: Wed Nov 18 11:33:53 CET 2015
[INFO] Final Memory: 9M/429M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project pride-inspector: Could not resolve dependencies for project uk.ac.ebi.pride.toolsuite:pride-inspector:jar:2.5.0-SNAPSHOT: The following artifacts could not be resolved: uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT, uk.ac.ebi.pride.tools:mzdata-parser:jar:1.2.2-SNAPSHOT, uk.a
c.ebi.pride.jaxb:pride-jaxb:jar:1.0.13-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-mzgraph-browser:jar:2.0.2-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-quality-chart:jar:2.0.3-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-swing-utils:jar:2.0.2-SNAPSHOT, uk.ac.ebi.pride.utilities:pride-utilities:jar:2.0.5-SNAPSHOT,
uk.ac.ebi.pride.utilities:pride-protein-inference:jar:0.0.5-SNAPSHOT, com.asperasoft:aspera-faspmanager:jar:2.7.0.42750: Failure to find uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT in http://pride-proteome.sourceforge.net/maven2 was cached in the local repository, resolution will not be reattempted until the updat
e interval of PRIDE_SourceForge_Maven2_Repository has elapsed or updates are forced -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal on project pride-inspector: Could not resolve dependencies for project uk.ac.ebi.pride.toolsuite:pride-inspector:jar:2.5.0-SNAPSHOT: The following artifacts could not be resolved: uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT, uk.ac.ebi.pr
ide.tools:mzdata-parser:jar:1.2.2-SNAPSHOT, uk.ac.ebi.pride.jaxb:pride-jaxb:jar:1.0.13-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-mzgraph-browser:jar:2.0.2-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-quality-chart:jar:2.0.3-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-swing-utils:jar:2.0.2-SNAPSHOT, uk.ac.ebi.pri
de.utilities:pride-utilities:jar:2.0.5-SNAPSHOT, uk.ac.ebi.pride.utilities:pride-protein-inference:jar:0.0.5-SNAPSHOT, com.asperasoft:aspera-faspmanager:jar:2.7.0.42750: Failure to find uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT in http://pride-proteome.sourceforge.net/maven2 was cached in the local repository, re
solution will not be reattempted until the update interval of PRIDE_SourceForge_Maven2_Repository has elapsed or updates are forced
at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies(LifecycleDependencyResolver.java:210)
at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies(LifecycleDependencyResolver.java:117)
at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved(MojoExecutor.java:258)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:201)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:537)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:196)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:141)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:290)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:230)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:409)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:352)
Caused by: org.apache.maven.project.DependencyResolutionException: Could not resolve dependencies for project uk.ac.ebi.pride.toolsuite:pride-inspector:jar:2.5.0-SNAPSHOT: The following artifacts could not be resolved: uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT, uk.ac.ebi.pride.tools:mzdata-parser:jar:1.2.2-SNAPSH
OT, uk.ac.ebi.pride.jaxb:pride-jaxb:jar:1.0.13-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-mzgraph-browser:jar:2.0.2-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-quality-chart:jar:2.0.3-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-swing-utils:jar:2.0.2-SNAPSHOT, uk.ac.ebi.pride.utilities:pride-utilities:jar:2.0.5-S
NAPSHOT, uk.ac.ebi.pride.utilities:pride-protein-inference:jar:0.0.5-SNAPSHOT, com.asperasoft:aspera-faspmanager:jar:2.7.0.42750: Failure to find uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT in http://pride-proteome.sourceforge.net/maven2 was cached in the local repository, resolution will not be reattempted until t
he update interval of PRIDE_SourceForge_Maven2_Repository has elapsed or updates are forced
at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve(DefaultProjectDependenciesResolver.java:189)
at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies(LifecycleDependencyResolver.java:185)
... 22 more
Caused by: org.sonatype.aether.resolution.DependencyResolutionException: The following artifacts could not be resolved: uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT, uk.ac.ebi.pride.tools:mzdata-parser:jar:1.2.2-SNAPSHOT, uk.ac.ebi.pride.jaxb:pride-jaxb:jar:1.0.13-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-mzgrap
h-browser:jar:2.0.2-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-quality-chart:jar:2.0.3-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-swing-utils:jar:2.0.2-SNAPSHOT, uk.ac.ebi.pride.utilities:pride-utilities:jar:2.0.5-SNAPSHOT, uk.ac.ebi.pride.utilities:pride-protein-inference:jar:0.0.5-SNAPSHOT, com.asperasoft:asper
a-faspmanager:jar:2.7.0.42750: Failure to find uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT in http://pride-proteome.sourceforge.net/maven2 was cached in the local repository, resolution will not be reattempted until the update interval of PRIDE_SourceForge_Maven2_Repository has elapsed or updates are forced
at org.sonatype.aether.impl.internal.DefaultRepositorySystem.resolveDependencies(DefaultRepositorySystem.java:375)
at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve(DefaultProjectDependenciesResolver.java:183)
... 23 more
Caused by: org.sonatype.aether.resolution.ArtifactResolutionException: The following artifacts could not be resolved: uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT, uk.ac.ebi.pride.tools:mzdata-parser:jar:1.2.2-SNAPSHOT, uk.ac.ebi.pride.jaxb:pride-jaxb:jar:1.0.13-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-mzgraph-
browser:jar:2.0.2-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-quality-chart:jar:2.0.3-SNAPSHOT, uk.ac.ebi.pride.toolsuite:inspector-swing-utils:jar:2.0.2-SNAPSHOT, uk.ac.ebi.pride.utilities:pride-utilities:jar:2.0.5-SNAPSHOT, uk.ac.ebi.pride.utilities:pride-protein-inference:jar:0.0.5-SNAPSHOT, com.asperasoft:aspera-
faspmanager:jar:2.7.0.42750: Failure to find uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT in http://pride-proteome.sourceforge.net/maven2 was cached in the local repository, resolution will not be reattempted until the update interval of PRIDE_SourceForge_Maven2_Repository has elapsed or updates are forced
at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:538)
at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:216)
at org.sonatype.aether.impl.internal.DefaultRepositorySystem.resolveDependencies(DefaultRepositorySystem.java:358)
... 24 more
Caused by: org.sonatype.aether.transfer.ArtifactNotFoundException: Failure to find uk.ac.ebi.jmzidml:jmzidentml:jar:1.2.3-SNAPSHOT in http://pride-proteome.sourceforge.net/maven2 was cached in the local repository, resolution will not be reattempted until the update interval of PRIDE_SourceForge_Maven2_Repository has e
lapsed or updates are forced
at org.sonatype.aether.impl.internal.DefaultUpdateCheckManager.newException(DefaultUpdateCheckManager.java:230)
at org.sonatype.aether.impl.internal.DefaultUpdateCheckManager.checkArtifact(DefaultUpdateCheckManager.java:204)
at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:427)
... 26 more
[ERROR]
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException

Add basic quantitation information for mzTab files.

Computing the protein inference in the MyriMatch example file took very long. It would be good if some kind of progress bar was shown. Or maybe the text "Loading file..." could change (f.e. "Computing protein inference...", "Loading identifications..."). At the moment, I'm just looking at the screen without any feedback of what's happening. Since it took too long I tried to kill the task clicking on the lower right progress bar and clicked the "x" next to the task but the computer was still running at 100% CPU. Also, closing the file didn't change anything. In the end, I had to kill the Inspector.#

Here you can find the file that was tested:
http://www.ebi.ac.uk/~yperez/111405_075_Mix_1_01.mzid

• By default when we open the popup the clicking behaviour of the mouse should be enable to select nodes.
• At the same time it would be great if the protein select in the protein table when the users click in the Protein Group button is select by default in the protein group panel and the PSM table is populated with the psms. Do not look very nice the empty table at the beginning.

If some details in the metadata cannot be access, explain why using “tooltips”, when hoovering the mouse over that type of data. For instance, instrument information cannot be shown if only mzIdentML files are present.

For most inferences, it is possible to give a rough estimation of the progress.
This might not be linear in time, but in calculated groups. But this is more or less normal in progress bars etc. I guess.
If we should add something like this, please give a comment here.

For the Missed Tryptic Cleavages, Peaks per MS/MS Spectrum, and Peak Intensity barcharts, the label above the highest bar is not visible, because the y-axis maximum isn't high enough. This only applies to the chart thumbnails view.

In the near future we will remove the Database Intance, It would be interesting in the near future to create the controllers inside PRIDE Inspector for WebServices.

When opening the MSGF+ example, the MGF file wasn't shown in the selection box since ".gz" is not included. I then selected "show all files" and selected the ".gz" file. It didn't display any error message but also didn't load any spectra. The only way to add spectra was to manually unzip the file, close the mzIdentML file and reopen it again. It would be nicer if this could be invoked through some button from within the GUI (f.e. set spectra files).

It would be nice to have a global filter for the experiment based on PSM scores.

To make more of the visualization, pulling in all connected elements from within the file (like building a real "PIA cluster") would be useful. At the moment only the elements, which are within the reported ProteinAmbiguityGroup, are shown in the visualization.

decrease the size of the letter to earn some space and use Sparkline.

The screen should be smoothly handled

We should add another button or custom panel to decide if we want to have or not protein inference information instead of running the protein inference when is not present in the file by default.

It would be interesting for those files without Decoy annotations, to highlight and set the decoy properties in order to filter and plot decoy information.

The ProteinGroup View has some inconsistencies for me. In the case of Peptide sequences, the number don’t fit with the total number or the total number of unique sequences (as PSMs).

Some bugs remainder: at some point when you select the peptide and change the layout i was unable to select again the any object. Rigth now as far as I see we have only one protein group every time we click the panel, then make sense to have the circle if wee know in advance that all the proteins are in the same group? How we can know which peptides are share by the same proteins?

When you download the files in the folder aspera/bin/ the permission should be changed to executable files using:
chmod 755 *
It will change the permission to all the executables.

When opening the MSGF+ example, the MGF file wasn't shown in the selection box since ".gz" is not included. I then selected "show all files" and selected the ".gz" file. It didn't display any error message but also didn't load any spectra. The only way to add spectra was to manually unzip the file, close the mzIdentML file and reopen it again. It would be nicer if this could be invoked through some button from within the GUI (f.e. set spectra files).

Search archive function: when I entered "melanoma" the list didn't change. Still, all projects were being displayed (screenshot 4). The download dialog didn't provide me with a quick option to only select "RESULT files", also, a "de-select all" button is missing. I had to manually de-select ~70 RAW files. This is not very nice. The download then didn't start and the GUI didn't show any error message. I only discovered this on the command line:

uk.ac.ebi.pride.toolsuite.gui.task.impl.AsperaDownloadTask@59360e80 failed on : com.asperasoft.faspmanager.LaunchException: Error starting transfer process: Failed to start process
com.asperasoft.faspmanager.LaunchException: Error starting transfer process: Failed to start process
at com.asperasoft.faspmanager.Session.start(Session.java:725) ~[aspera-faspmanager-2.7.0.42750.jar:2.7.0.42750 ]
at com.asperasoft.faspmanager.FaspManager.startTransfer(FaspManager.java:768) ~[aspera-faspmanager-2.7.0.42750.jar:2.7.0.42750 ]
at com.asperasoft.faspmanager.FaspManager.startTransfer(FaspManager.java:736) ~[aspera-faspmanager-2.7.0.42750.jar:2.7.0.42750 ]
at uk.ac.ebi.pride.toolsuite.gui.aspera.AsperaFileUploader.downloadFiles(AsperaFileUploader.java:180) ~[pride-inspector-2.5.0-SNAPSHOT.jar:na]
at uk.ac.ebi.pride.toolsuite.gui.task.impl.AsperaDownloadTask.asperaUpload(AsperaDownloadTask.java:81) ~[pride-inspector-2.5.0-SNAPSHOT.jar:na]
at uk.ac.ebi.pride.toolsuite.gui.task.impl.AsperaDownloadTask.doInBackground(AsperaDownloadTask.java:41) ~[pride-inspector-2.5.0-SNAPSHOT.jar:na]
at uk.ac.ebi.pride.toolsuite.gui.task.impl.AsperaDownloadTask.doInBackground(AsperaDownloadTask.java:26) ~[pride-inspector-2.5.0-SNAPSHOT.jar:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:296) ~[na:1.7.0_65]
at java.util.concurrent.FutureTask.run(FutureTask.java:262) ~[na:1.7.0_65]
at javax.swing.SwingWorker.run(SwingWorker.java:335) ~[na:1.7.0_65]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) ~[na:1.7.0_65]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) ~[na:1.7.0_65]
at java.lang.Thread.run(Thread.java:745) ~[na:1.7.0_65]

Integrate the exporter from ms-data-core-api to mztab

For some users it would be interesting to add protein sequence databases in FASTA format to check the quality of the experiment, some of the advantages are:

• We will be able to visualise decoy proteins.
• Visualise those proteins without sequence in Uniprot for example REqSEq proteins.

In Protein table, the header of the columns should use PSMs instead of peptides

Decide and implement one chart for quatitation quality assessment

Here is the exception:

2014-11-06 09:37:58,225 ERROR [AWT-EventQueue-0] u.a.e.p.u.d.c.i.C.PrideXmlControllerImpl [PrideXmlControllerImpl.java:438] Error while getting spectrum: 318
java.lang.NullPointerException: null
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.PrideXmlControllerImpl.getSpectrumById(PrideXmlControllerImpl.java:432) ~[ms-data-core-api-0.11.25-SNAPSHOT.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController.getSpectrumById(CachedDataAccessController.java:154) [ms-data-core-api-0.11.25-SNAPSHOT.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController.getSpectrumPrecursorMz(AbstractDataAccessController.java:220) [ms-data-core-api-0.11.25-SNAPSHOT.jar:na]
at uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController.getSpectrumPrecursorMz(CachedDataAccessController.java:308) [ms-data-core-api-0.11.25-SNAPSHOT.jar:na]
at uk.ac.ebi.pride.toolsuite.gui.component.mzgraph.FragmentationTablePane.isOverflow(FragmentationTablePane.java:119) [classes/:na]
at uk.ac.ebi.pride.toolsuite.gui.component.mzgraph.FragmentationTablePane.succeed(FragmentationTablePane.java:192) [classes/:na]
at uk.ac.ebi.pride.toolsuite.gui.task.Task.fireSucceedListeners(Task.java:313) [classes/:na]
at uk.ac.ebi.pride.toolsuite.gui.task.Task.fireCompletionListeners(Task.java:281) [classes/:na]
at uk.ac.ebi.pride.toolsuite.gui.task.Task.access$300(Task.java:27) [classes/:na]
at uk.ac.ebi.pride.toolsuite.gui.task.Task$TaskStateMonitor$1.run(Task.java:392) [classes/:na]
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:251) [na:1.7.0_05]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:701) [na:1.7.0_05]
at java.awt.EventQueue.access$000(EventQueue.java:102) [na:1.7.0_05]
at java.awt.EventQueue$3.run(EventQueue.java:662) [na:1.7.0_05]
at java.awt.EventQueue$3.run(EventQueue.java:660) [na:1.7.0_05]
at java.security.AccessController.doPrivileged(Native Method) [na:1.7.0_05]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) [na:1.7.0_05]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:671) [na:1.7.0_05]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:244) [na:1.7.0_05]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:163) [na:1.7.0_05]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:151) [na:1.7.0_05]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:147) [na:1.7.0_05]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:139) [na:1.7.0_05]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:97) [na:1.7.0_05]
2014-11-06 09:37:58,226 ERROR [AWT-EventQueue-0] u.a.e.p.t.g.c.m.FragmentationTablePane [FragmentationTablePane.java:136] Error while getting spectrum: 318

I used for the testing the same files I have always used. Mascot F002870.mid with and without MS/MS annotations plus the corresponding mgf file. They should be in the list of examples that are stored somewhere in the internal file system. They are not in Github, as far as I could see.

1-For these two files the quality charts don’t get generated (I killed the process after 10 min twice).
2- Also for the Decoy filter, it is not possible to come back to the initial status (“Remove” filter).

Visualisation of protein groups for those files that contains protein groups information (mzIdentml).