Thanks David, I'm certain PeptideProphet is finishing without error (I've tested in many times.). It's just that it produces fewer XML attributes in the root msms_pipeline_analysis node than InterProphet does. Because of these missing attributes, PeptideProphet results are not being successfully validated (by some software) and InterProphet results are. The exact syntax is in my post, but adding xmlns="http://regis-web.systemsbiology.net/pepXML"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; to the msms_pipeline_analysis node in the PepXML output by PeptideProphet should solve the problem (it's already there in the InterProphet output).
Mike On Thursday, February 21, 2019 at 3:47:43 PM UTC-8, David Shteynberg wrote: > > Hi Mike, > > It sounds like either PeptideProphet crashed and generated incomplete > pepXML or another program upstream of PeptideProphet failed partly > through. Can you check the standard and error outputs carefully for any > clues? Let me know what you find. > > David > > On Thu, Feb 21, 2019, 12:22 PM Michael Riffle <[email protected] > <javascript:> wrote: > >> Running TPP v5.2.0-b1 Flammagenitus Pre-release Beta, Build >> 201809101205-7809 (Linux-x86_64)) >> >> Parsing pepXML files with Java using JAXB classes created from the schema >> (http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v122.xsd). >> >> >> I have noticed that PeptideProphet doesn't produce XML that can be >> successfully parsed but that InterProphet does. Here is the error produced >> from the PeptideProphet XML: >> >> [org.xml.sax.SAXParseException; systemId: >> file:interact-2018_Oct_4_EhuxDDA_DA06.pep.xml; lineNumber: 3; columnNumber: >> 253; The >> >> prefix "xsi" for attribute "xsi:schemaLocation" associated with an >> element type "msms_pipeline_analysis" is not bound.] >> >> >> The culprit is the <msms_pipeline_analysis> root element is missing vital >> attributes when run by peptideprophet. >> >> PeptideProphet element: >> <msms_pipeline_analysis xsi:schemaLocation=" >> http://regis-web.systemsbiology.net/pepXML >> /usr/local/tppschema/pepXML_v122.xsd" >> summary_xml="/data/mass_spec/mriffle/brook.magnum.results/interact-2018_Oct_4_EhuxDDA_DA06.pep.xml"> >> >> InterProphet element: >> <msms_pipeline_analysis xmlns="http://regis-web.systemsbiology.net/pepXML"; >> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; >> xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML >> /tools/bin/TPP/tpp/schema/pepXML_v122.xsd" >> summary_xml="/data/mass_spec/mriffle/brook.magnum.results/interact-2018_Oct_4_EhuxDDA_DA06.ipro.pep.xml"> >> >> If I add the following to the PeptideProphet msms_pipeline_analysis >> element it works and parses happily: >> xmlns="http://regis-web.systemsbiology.net/pepXML"; xmlns:xsi=" >> http://www.w3.org/2001/XMLSchema-instance"; >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
