Just to add to the info .. these are files that have been combined using the TPP tool iProphet. The original analysis was done using LabKey's built-in TPP and then the .pep.xml files copied over and combined using vanilla TPP.

Hello,

We attempt to offer the import on the most comprehensive file in the directory. For example, if a directory has results.pep.xml and results.prot.xml, we offer the import action on the .prot.xml file. Initiating that action will import both the .prot.xml and .pep.xml results. Similarly, if there's a .xar.xml (a LabKey-generated file that contains metadata about the analysis that generated the files), we'll prefer that as the import unit.

Additionally, the configuration for the project/folder controls which actions are available. Ensure that the MS2 module is enabled in the list on the right side of the page (even if the folder type is set to MS1 or something else) by going to Admin->Folder->Management and choosing the Folder Type tab.

Thanks,
Josh

Just an update to this issue. I've revisited my attempts to do this and when importing the prot.xml file get the following error

04 Sep 2014 13:12:07,854 INFO : Starting to load ProteinProphet file C:\Pipeline\files\ImportTest2\@files\Sample1C_1.prot.xml
04 Sep 2014 13:12:07,858 INFO : Resolved referenced PepXML file to C:\Pipeline\files\ImportTest2\@files\Sample1C_1.pep.xml
04 Sep 2014 13:12:07,859 INFO : Starting import from Sample1C_1.pep.xml
04 Sep 2014 13:12:07,867 INFO : Starting to clear out any previously imported data for Sample1C_1.pep.xml
04 Sep 2014 13:12:07,904 ERROR: MS2 import failed
java.lang.IllegalStateException: Current state is not among the states START_ELEMENT , ATTRIBUTEvalid for getAttributeValue()
java.lang.IllegalStateException: Current state is not among the states START_ELEMENT , ATTRIBUTEvalid for getAttributeValue()
    at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.getAttributeValue(Unknown Source)
    at org.labkey.api.reader.XMLStreamReaderWrapper.getAttributeValue(XMLStreamReaderWrapper.java:81)
    at org.labkey.ms2.reader.PeptideProphetSummary.load(PeptideProphetSummary.java:57)
    at org.labkey.ms2.reader.PepXmlLoader.readAnalysisSummaries(PepXmlLoader.java:66)
    at org.labkey.ms2.reader.PepXmlLoader.<init>(PepXmlLoader.java:42)
    at org.labkey.ms2.PepXmlImporter.importRun(PepXmlImporter.java:92)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:193)
    at org.labkey.ms2.MS2Manager.importRun(MS2Manager.java:611)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:596)
    at org.labkey.ms2.ProteinProphetImporter.importRun(ProteinProphetImporter.java:358)
    at org.labkey.ms2.ProteinProphetImporter.importFile(ProteinProphetImporter.java:81)
    at org.labkey.ms2.pipeline.ProteinProphetPipelineJob.run(ProteinProphetPipelineJob.java:69)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
04 Sep 2014 13:12:07,932 ERROR: ProteinProphet load failed
java.lang.IllegalStateException: Current state is not among the states START_ELEMENT , ATTRIBUTEvalid for getAttributeValue()

Hello,

This sounds like a potentially invalid XML file. Can you attach the pepXML file, or check that it appears to be well-formed?

Thanks,
Josh

Here's a prot.xml / pep.xml pair. I'm using TPP 4.7 rev1 and in this example 6 samples are combined using iProphet and then Protein Prophet performed on the results.

The issue seems to be related to pep.xml files generated with iProphet. If I don't use iProphet then it imports fine.

Here's the same 6 files combined without using iProphet. These import fine.

Hello,

Thanks for the files. I've investigated and identified two related issues present in the iProphet version of the files. I opened a bug to support this:

https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=21502

Thanks,
Josh