Hi Wonjong,

1. If you refer to merging all the results from 40 mzXML into a single result file, the cluster pipeline support this feature via the fraction protocol. (Mini-pipeline does not support this feature.) If you are referring to initiating the X!Tandem search on all 40 mzXML in a single search protocol definition, it is already supported in this manner currently via "X!Tandem Peptide Search" button when you click on "Process and Upload Data" button in "Pipeline" tab.

2. Yes, you can do that. You may also perform an import via "Pipeline" tab, "Process and Upload Data" button. Navigating the folders, buttons with the label "Import Peptides" for files with extension ".pep.xml" (pepXML) and with the label "Import ProteinProphet" for files with extension ".prot.xml" (protXML) will appear for you to do the same thing. However, the files have to be under the "Pipeline root directory" setup via the "Pipeline" tab.

*Chee-Hong.

Yes, unfortunately, what we call the "mini-pipeline" (where jobs run on the web server itself), which we ship as our default installation, and what we call the "cluster pipeline" differ in a number of ways. In fact, they are at this point almost completely separate code, written in Java and Perl respectively mad to act similarly.

Sadly, I am out sick, and won't be able to contribute for v1.7, but while convalescing I have finally realized how I should have done this all along, and hope to convert fairly quickly to a mostly shared code line between the two installation types. It is my hope that this could make v1.8. This version would contain the feature you request (support for multi-fraction runs) in the "mini-pipeline", as well as the "cluster pipeline" (where, as Chee-Hong points out, it already exists).

Sorry for the confusion. At this point you either need to do things manually as Chee-Hong suggests, or you need to alter your installation to use a cluster pipeline (only abailable, if you have a machine running a supported cluster scheduler for a functioning cluster).

Thank you Chee-Hong

I followed what you described in No. 2. I copied pepXML and protXML files to under the root directory. But these files did not show, there are no extension button 'import peptides', I see only mzXML files with 'search for peptides'.

Are the extension ".pep.xml" and ".prot.xml" respectively rather than .pepXML and .protXML or just .xml?
Which version of CPAS are you running?
*Chee-Hong.

Thank you. I changed file extension exactly what you told. '*.pep.xml' Now CPAS recognizes the files. Thank you very much.

I successfully loaded pepXML files ( I had to open the .pep.xml file with text editor and change the path to database fasta file).

I want to run ProteinProphet with a pepXML file. Where can I find the button to run ProteinProphet?

Chee-Hong said

1. If you refer to merging all the results from 40 mzXML into a single result file, the cluster pipeline support this feature via the fraction protocol.

How can I use 'fraction protocol'?
Thank you.

If you are running the cluster pipeline you can ask it to merge all of the mzXML files in a single directory into one batched pepXML file which will then get run through PeptideProphet, XPress (optionally), and ProteinProphet by doing one of the following:
1. Chose a 'FractionProtocol' during the "Process and Upload Data" step where you define the protocol used to gather you mzXML files.
2. Add the line:
<note type="input" label="pipeline, data type">Fractions</note>
to your X! Tandem parameters.
3. Add the line:
<note type="input" label="pipeline, data type">Both</note>
to your X! Tandem parameters. This will cause both fraction batching as well as separate processing of each mzXML file as a single sample. Some of the labs at the FHCRC requested this, and find it usefull for comparison.

Thank you for your response.
1. I do not have 'FracktionProtocol' yet. I type in 'FractionProtocol' for a new protocol name
2. Added <note type="input" label="pipeline, data type">Fractions</note> to my X! Tandem parameters.
I failed to upload mzXML files, could you help me, please?

From your response;
If you are running the cluster pipeline you can ask it to merge all of the mzXML files in a single directory into one batched pepXML file which will then get run through PeptideProphet, XPress (optionally), and ProteinProphet by doing one of the following:
------------------------------------------------------------------------------
I do not think I am doing cluster pipeline, I think I am doing minipipeline, since I just generated individual mzXML file and clicked 'search peptides'.
I really need to do what you described; one batched pepXML file, get through peptideProphet, proteinProphet, and to compare them all ('hierarchy show' display number of proteins, not proteinProphet style)
Thank you.


-------------------------------------------------------------------------------------------
17 Nov 2006 14:03:18,378 INFO : X! Tandem search for DSL01-081506-TZ-0199-GEL-FT-13.mzXML
17 Nov 2006 14:03:18,382 INFO : =======================================
17 Nov 2006 14:17:31,224 INFO : tandem.exe output
17 Nov 2006 14:17:31,225 INFO : =======================================
17 Nov 2006 14:17:31,227 INFO : running: tandem.exe input.xml
17 Nov 2006 14:17:31,302 INFO :
17 Nov 2006 14:17:31,304 INFO : X! TANDEM 2 (2006.09.15.1)
17 Nov 2006 14:17:31,306 INFO :
17 Nov 2006 14:17:36,463 INFO : Loading spectra ...... loaded.
17 Nov 2006 14:17:36,466 INFO : Spectra matching criteria = 11957
17 Nov 2006 14:17:36,468 INFO : Pluggable scoring enabled.
17 Nov 2006 14:17:36,470 INFO : Starting threads . started.
17 Nov 2006 14:17:36,472 INFO : Computing models:
17 Nov 2006 14:17:36,474 INFO :
17 Nov 2006 14:23:42,607 INFO : Spectrum-to-sequence matching process in progress | 50 ks
17 Nov 2006 14:29:24,155 INFO : Spectrum-to-sequence matching process in progress | 100 ks
17 Nov 2006 14:31:27,799 INFO : Spectrum-to-
17 Nov 2006 14:31:27,811 INFO :
17 Nov 2006 14:31:27,814 INFO : kilosequences modelled = 111
17 Nov 2006 14:31:27,884 INFO : Model refinement:
17 Nov 2006 14:31:27,886 INFO : Creating report:
17 Nov 2006 14:31:27,974 INFO :     initial calculations ..... done.
17 Nov 2006 14:31:27,977 INFO :     sorting ..... done.
17 Nov 2006 14:31:41,297 INFO :     finding repeats ..... done.
17 Nov 2006 14:31:41,305 INFO :     evaluating results ..... done.
17 Nov 2006 14:31:41,857 INFO :     calculating expectations ..... done.
17 Nov 2006 14:31:50,231 INFO :     writing results ..... done.
17 Nov 2006 14:31:50,306 INFO :
17 Nov 2006 14:31:50,311 INFO : Valid models = 238
17 Nov 2006 14:31:50,315 INFO :
17 Nov 2006 14:31:50,319 INFO :
17 Nov 2006 14:31:50,343 INFO : Tandem2XML output
17 Nov 2006 14:31:50,344 INFO : =======================================
17 Nov 2006 14:31:50,346 INFO : running: Tandem2XML /proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13.xtan.xml /proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13-raw.pep.xml
17 Nov 2006 14:31:55,690 INFO : xinteract output
17 Nov 2006 14:31:55,693 INFO : =======================================
17 Nov 2006 14:31:55,695 INFO : running: xinteract -p0 -Opt -nR -NDSL01-081506-TZ-0199-GEL-FT-13.pep.xml /proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13-raw.pep.xml
17 Nov 2006 14:31:55,767 INFO :
17 Nov 2006 14:31:55,771 INFO : /usr/local/tpp/bin/xinteract (TPP v2.9 GALE rev.3, Build 200610171545)
17 Nov 2006 14:31:55,773 INFO :
17 Nov 2006 14:31:55,775 INFO : running: "InteractParser DSL01-081506-TZ-0199-GEL-FT-13.pep.xml '/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13-raw.pep.xml'"
17 Nov 2006 14:31:55,793 INFO : file 1: /proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13-raw.pep.xml
17 Nov 2006 14:32:02,867 INFO : processed altogether 10506 results
17 Nov 2006 14:32:06,971 INFO : command completed in 11 sec
17 Nov 2006 14:32:06,992 INFO :
17 Nov 2006 14:32:07,006 INFO : running: "PeptideProphetParser DSL01-081506-TZ-0199-GEL-FT-13.pep.xml MINPROB=0"
17 Nov 2006 14:32:07,010 INFO : (X! Tandem) (minprob 0)
17 Nov 2006 14:32:07,013 INFO : init with X! Tandem trypsin
17 Nov 2006 14:32:12,243 INFO : MS Instrument info: Manufacturer: ThermoFinnigan, Model: LTQ, Ionization: ESI, Analyzer: Ion Trap, Detector: EMT
17 Nov 2006 14:32:12,247 INFO :
17 Nov 2006 14:32:12,254 INFO : PeptideProphet v3.0 April 1, 2004 (TPP v2.9 GALE rev.3, Build 200610171545) AKeller@ISB
17 Nov 2006 14:32:12,256 INFO : read in 1371 1+, 4546 2+, and 4589 3+ spectra
17 Nov 2006 14:32:12,498 INFO : iteration 1 2 3 4 5 6 7 8 9 10 11 12 13 model complete after 14 iterations
17 Nov 2006 14:32:20,920 INFO : command completed in 14 sec
17 Nov 2006 14:32:20,935 INFO :
17 Nov 2006 14:32:20,939 INFO : running: ""ProteinProphet.pl" DSL01-081506-TZ-0199-GEL-FT-13.pep.xml DSL01-081506-TZ-0199-GEL-FT-13.pep-prot.shtml XML_INPUT NOPLOT"
17 Nov 2006 14:32:21,138 INFO :
17 Nov 2006 14:32:21,143 INFO : ProteinProphet.pl v2.0 (TPP v2.9 GALE rev.3, Build 200610171545) AKeller August 15, 2003 (xml input) (using degen pep info)
17 Nov 2006 14:32:21,145 INFO : Calling /usr/local/tpp/bin/DatabaseParser "/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13.pep.xml"
17 Nov 2006 14:32:23,517 INFO : processing /proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13.pep.xml ... read in 39 1+, 297 2+, and 0 3+ spectra with min prob 0.05
17 Nov 2006 14:32:26,922 INFO : Reading results.
17 Nov 2006 14:32:26,941 INFO : sh: batchcoverage: command not found
17 Nov 2006 14:32:27,447 INFO : command completed in 7 sec
17 Nov 2006 14:32:27,451 INFO : InteractParser DSL01-081506-TZ-0199-GEL-FT-13.pep.xml '/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13-raw.pep.xml' 11 sec
17 Nov 2006 14:32:27,453 INFO : PeptideProphetParser DSL01-081506-TZ-0199-GEL-FT-13.pep.xml MINPROB=0 14 sec
17 Nov 2006 14:32:27,455 INFO : "ProteinProphet.pl" DSL01-081506-TZ-0199-GEL-FT-13.pep.xml DSL01-081506-TZ-0199-GEL-FT-13.pep-prot.shtml XML_INPUT NOPLOT 7 sec
17 Nov 2006 14:32:27,456 INFO : job completed in 32 sec
17 Nov 2006 14:32:27,529 INFO : Existing protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XTandemSearch:2' is referenced by other experiment runs, so it cannot be updated
17 Nov 2006 14:32:27,536 INFO : Existing protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.ConvertToPepXml:2' is referenced by other experiment runs, so it cannot be updated
17 Nov 2006 14:32:27,544 INFO : Existing protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XInteract.PeptideProphet:2' is referenced by other experiment runs, so it cannot be updated
17 Nov 2006 14:32:27,550 INFO : Existing protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XInteract.ProteinProphet:2' is referenced by other experiment runs, so it cannot be updated
17 Nov 2006 14:32:27,556 INFO : Existing protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XTandemAnalysis:3' is referenced by other experiment runs, so it cannot be updated
17 Nov 2006 14:32:27,562 INFO : Existing protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MarkRunOutput:2' is referenced by other experiment runs, so it cannot be updated
17 Nov 2006 14:32:27,569 INFO : Finished loading Experiment with LSID 'urn:lsid:sbri.org:Experiment.Folder-52:DefaultExperiment'
17 Nov 2006 14:32:27,589 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XTandemSearch:2'
17 Nov 2006 14:32:27,598 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.ConvertToPepXml:2'
17 Nov 2006 14:32:27,607 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XInteract.PeptideProphet:2'
17 Nov 2006 14:32:27,616 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XInteract.ProteinProphet:2'
17 Nov 2006 14:32:27,628 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XTandemAnalysis:3'
17 Nov 2006 14:32:27,635 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MarkRunOutput:2'
17 Nov 2006 14:32:27,699 INFO : Found an existing entry for Data LSID urn:lsid:sbri.org:Data.Folder-52-Xar-58947dac-4c10-1029-b4e8-f528764dc076:..%2FDSL01-081506-TZ-0199-GEL-FT-13.mzXML, not reloading its values from scratch
17 Nov 2006 14:32:27,701 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Folder-52-Xar-58947dac-4c10-1029-b4e8-f528764dc076:..%2FDSL01-081506-TZ-0199-GEL-FT-13.mzXML'
17 Nov 2006 14:32:27,713 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Folder-52-Xar-58947dc1-4c10-1029-b4e8-f528764dc076:tandem.xml'
17 Nov 2006 14:32:27,720 INFO : Found an existing entry for Data LSID urn:lsid:sbri.org:Data.Folder-52-Xar-58947db4-4c10-1029-b4e8-f528764dc076:..%2F..%2F..%2Fdatabases%2Fsequences_HuPf_052506.fasta, not reloading its values from scratch
17 Nov 2006 14:32:27,721 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Folder-52-Xar-58947db4-4c10-1029-b4e8-f528764dc076:..%2F..%2F..%2Fdatabases%2Fsequences_HuPf_052506.fasta'
17 Nov 2006 14:32:27,836 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XTandemAnalysis:3'
17 Nov 2006 14:32:27,875 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Run-160:XTanFile'
17 Nov 2006 14:32:27,876 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XTandemSearch:2'
17 Nov 2006 14:32:27,910 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Run-160:PepXmlFile'
17 Nov 2006 14:32:27,913 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.ConvertToPepXml:2'
17 Nov 2006 14:32:27,943 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Run-160:ScoredPepXmlFile'
17 Nov 2006 14:32:27,945 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XInteract.PeptideProphet:2'
17 Nov 2006 14:32:27,979 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Run-160:ProteinScoresFile'
17 Nov 2006 14:32:27,981 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XInteract.ProteinProphet:2'
17 Nov 2006 14:32:27,995 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MarkRunOutput:2'
17 Nov 2006 14:32:27,996 INFO : Finished loading ExperimentRun with LSID 'urn:lsid:sbri.org:ExperimentRun.Folder-52:MS2-xtandem%2FFractionProtocol%2FDSL01-081506-TZ-0199-GEL-FT-13'
17 Nov 2006 14:32:28,002 INFO : Trying to load data file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/tandem.xml into the system
17 Nov 2006 14:32:28,013 INFO : No experiment data handler registered for mime type text/xml on file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/tandem.xml, no special loading will be done on this file.
17 Nov 2006 14:32:28,017 INFO : Finished trying to load data file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/tandem.xml into the system
17 Nov 2006 14:32:28,021 INFO : Trying to load data file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.xtan.xml into the system
17 Nov 2006 14:32:28,030 INFO : No experiment data handler registered for mime type text/xml on file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.xtan.xml, no special loading will be done on this file.
17 Nov 2006 14:32:28,035 INFO : Finished trying to load data file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.xtan.xml into the system
17 Nov 2006 14:32:28,039 INFO : Trying to load data file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/FractionProtocol/DSL01-081506-TZ-0199-GEL-FT-13.pep.xml into the system
17 Nov 2006 14:32:28,079 INFO : prepareRun: Starting upload from "DSL01-081506-TZ-0199-GEL-FT-13.pep.xml"
17 Nov 2006 14:32:28,099 INFO : Clearing out existing MS2 data for DSL01-081506-TZ-0199-GEL-FT-13.pep.xml
17 Nov 2006 14:32:28,129 INFO : Finished clearing out existing MS2 data for DSL01-081506-TZ-0199-GEL-FT-13.pep.xml
17 Nov 2006 14:32:28,164 ERROR: XMLStreamException in next()
com.ctc.wstx.exc.WstxParsingException: Unexpected close tag </search_summary>; expected </parameter>.
 at [row,col {unknown-source}]: [371,16]
    at com.ctc.wstx.sr.StreamScanner.throwParseError(StreamScanner.java:396)
    at com.ctc.wstx.sr.WstxStreamReader.reportWrongEndElem(WstxStreamReader.java:3078)
    at com.ctc.wstx.sr.WstxStreamReader.readEndElem(WstxStreamReader.java:3020)
    at com.ctc.wstx.sr.WstxStreamReader.nextFromTree(WstxStreamReader.java:2682)
    at com.ctc.wstx.sr.WstxStreamReader.next(WstxStreamReader.java:971)
    at org.fhcrc.cpas.tools.XMLStreamReaderWrapper.next(XMLStreamReaderWrapper.java:246)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.handleSearchSummary(PepXmlLoader.java:201)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.assembleRunInfo(PepXmlLoader.java:178)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.getNextFraction(PepXmlLoader.java:152)
    at org.fhcrc.cpas.tools.PepXmlLoader$FractionIterator.next(PepXmlLoader.java:119)
    at org.fhcrc.cpas.ms2.PepXmlImporter.uploadRun(PepXmlImporter.java:90)
    at org.fhcrc.cpas.ms2.MS2Importer.upload(MS2Importer.java:181)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:367)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:356)
    at org.fhcrc.cpas.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:93)
    at org.fhcrc.cpas.exp.XarReader.loadDataFile(XarReader.java:921)
    at org.fhcrc.cpas.exp.XarReader.loadDoc(XarReader.java:340)
    at org.fhcrc.cpas.exp.XarReader.parseAndLoad(XarReader.java:164)
    at org.fhcrc.cpas.exp.XarReader.uploadRun(XarReader.java:116)
    at org.fhcrc.cpas.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:124)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.search(XTandemPipelineJob.java:584)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.run(XTandemPipelineJob.java:189)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
    at java.util.concurrent.FutureTask.run(FutureTask.java:123)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:168)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
    at java.lang.Thread.run(Thread.java:595)
17 Nov 2006 14:32:28,167 ERROR: MS2 data upload failed
java.lang.RuntimeException: XMLStreamException in next()
    at org.fhcrc.cpas.tools.PepXmlLoader$FractionIterator.next(PepXmlLoader.java:124)
    at org.fhcrc.cpas.ms2.PepXmlImporter.uploadRun(PepXmlImporter.java:90)
    at org.fhcrc.cpas.ms2.MS2Importer.upload(MS2Importer.java:181)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:367)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:356)
    at org.fhcrc.cpas.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:93)
    at org.fhcrc.cpas.exp.XarReader.loadDataFile(XarReader.java:921)
    at org.fhcrc.cpas.exp.XarReader.loadDoc(XarReader.java:340)
    at org.fhcrc.cpas.exp.XarReader.parseAndLoad(XarReader.java:164)
    at org.fhcrc.cpas.exp.XarReader.uploadRun(XarReader.java:116)
    at org.fhcrc.cpas.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:124)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.search(XTandemPipelineJob.java:584)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.run(XTandemPipelineJob.java:189)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
    at java.util.concurrent.FutureTask.run(FutureTask.java:123)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:168)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
    at java.lang.Thread.run(Thread.java:595)
Caused by: com.ctc.wstx.exc.WstxParsingException: Unexpected close tag </search_summary>; expected </parameter>.
 at [row,col {unknown-source}]: [371,16]
    at com.ctc.wstx.sr.StreamScanner.throwParseError(StreamScanner.java:396)
    at com.ctc.wstx.sr.WstxStreamReader.reportWrongEndElem(WstxStreamReader.java:3078)
    at com.ctc.wstx.sr.WstxStreamReader.readEndElem(WstxStreamReader.java:3020)
    at com.ctc.wstx.sr.WstxStreamReader.nextFromTree(WstxStreamReader.java:2682)
    at com.ctc.wstx.sr.WstxStreamReader.next(WstxStreamReader.java:971)
    at org.fhcrc.cpas.tools.XMLStreamReaderWrapper.next(XMLStreamReaderWrapper.java:246)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.handleSearchSummary(PepXmlLoader.java:201)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.assembleRunInfo(PepXmlLoader.java:178)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.getNextFraction(PepXmlLoader.java:152)
    at org.fhcrc.cpas.tools.PepXmlLoader$FractionIterator.next(PepXmlLoader.java:119)
    ... 20 more
17 Nov 2006 14:32:28,172 FATAL: Exception during load
java.lang.RuntimeException: XMLStreamException in next()
    at org.fhcrc.cpas.tools.PepXmlLoader$FractionIterator.next(PepXmlLoader.java:124)
    at org.fhcrc.cpas.ms2.PepXmlImporter.uploadRun(PepXmlImporter.java:90)
    at org.fhcrc.cpas.ms2.MS2Importer.upload(MS2Importer.java:181)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:367)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:356)
    at org.fhcrc.cpas.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:93)
    at org.fhcrc.cpas.exp.XarReader.loadDataFile(XarReader.java:921)
    at org.fhcrc.cpas.exp.XarReader.loadDoc(XarReader.java:340)
    at org.fhcrc.cpas.exp.XarReader.parseAndLoad(XarReader.java:164)
    at org.fhcrc.cpas.exp.XarReader.uploadRun(XarReader.java:116)
    at org.fhcrc.cpas.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:124)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.search(XTandemPipelineJob.java:584)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.run(XTandemPipelineJob.java:189)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
    at java.util.concurrent.FutureTask.run(FutureTask.java:123)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:168)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
    at java.lang.Thread.run(Thread.java:595)
Caused by: com.ctc.wstx.exc.WstxParsingException: Unexpected close tag </search_summary>; expected </parameter>.
 at [row,col {unknown-source}]: [371,16]
    at com.ctc.wstx.sr.StreamScanner.throwParseError(StreamScanner.java:396)
    at com.ctc.wstx.sr.WstxStreamReader.reportWrongEndElem(WstxStreamReader.java:3078)
    at com.ctc.wstx.sr.WstxStreamReader.readEndElem(WstxStreamReader.java:3020)
    at com.ctc.wstx.sr.WstxStreamReader.nextFromTree(WstxStreamReader.java:2682)
    at com.ctc.wstx.sr.WstxStreamReader.next(WstxStreamReader.java:971)
    at org.fhcrc.cpas.tools.XMLStreamReaderWrapper.next(XMLStreamReaderWrapper.java:246)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.handleSearchSummary(PepXmlLoader.java:201)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.assembleRunInfo(PepXmlLoader.java:178)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.getNextFraction(PepXmlLoader.java:152)
    at org.fhcrc.cpas.tools.PepXmlLoader$FractionIterator.next(PepXmlLoader.java:119)
    ... 20 more
17 Nov 2006 14:32:28,173 FATAL: Upload FAILED

I am afraid you are in a bind that won't be solved until our next release sometime in 2007 (February? March?)

Unless you get the cluster pipeline working at your site, you will have to do this all manually. If you can work with folks on the Sashimi / Trans Proteomic Pipeline project to understand how to use the tools well enought to produce your single pepXML file from multiple mzXML sources, then you could upload that into CPAS.

Actually you can run CPAS, and start with the .xtan.xml files of the resulting searches. You would then run Tandem2XML to get raw pepXML files, followed by a call to xinteract to get everything batched and run through PeptideProphet and ProteinProphet.

But really you are asking a lot for free support. If you don't have a cluster, and are stuck with the "Trial Installation" on a single machine, then you are going to have to be creative for now.