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]. 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.
