--- a/test-data/small-index-filter.mzML	Wed Dec 07 16:43:07 2016 -0500
+++ b/test-data/small-index-filter.mzML	Sat Feb 23 06:25:48 2019 -0500
@@ -2,8 +2,8 @@
 <indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
   <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="small" version="1.1.0">
     <cvList count="2">
-      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
-      <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>
     </cvList>
     <fileDescription>
       <fileContent>
@@ -11,7 +11,7 @@
         <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
       </fileContent>
       <sourceFileList count="3">
-        <sourceFile id="RAW1" name="small.RAW" location="file:///C:\pwiz-src\trunk\pwiz\example_data">
+        <sourceFile id="RAW1" name="small.RAW" location="file:///">
           <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
           <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>
           <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>
@@ -20,7 +20,7 @@
           <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>
         </sourceFile>
         <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">
-          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -30,14 +30,17 @@
         <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>
       </referenceableParamGroup>
     </referenceableParamGroupList>
-    <softwareList count="3">
+    <softwareList count="4">
       <software id="Xcalibur" version="1.1 Beta 7">
         <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
       </software>
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.8990" version="3.0.8990">
+      <software id="pwiz_3.0.19038" version="3.0.19038">
+        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
+      </software>
+      <software id="pwiz_3.0.19044" version="3.0.19044">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +85,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.8990">
+        <processingMethod order="0" softwareRef="pwiz_3.0.19038">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.8990">
+        <processingMethod order="1" softwareRef="pwiz_3.0.19038">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -496,18 +499,18 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
-      <offset idRef="controllerType=0 controllerNumber=1 scan=3">5577</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=4">14148</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=5">26006</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=11">36522</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=14">47993</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=15">57476</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=16">65257</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=3">5697</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=4">14268</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=5">26126</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=11">36642</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=14">48113</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=15">57596</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=16">65377</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">76395</offset>
+      <offset idRef="TIC">76515</offset>
     </index>
   </indexList>
-  <indexListOffset>78345</indexListOffset>
-  <fileChecksum>0d5bbd9cad4ad9471eba2e80d0ddea2cddcf3db9</fileChecksum>
+  <indexListOffset>78465</indexListOffset>
+  <fileChecksum>0671bee5b37c6f8cc8afde991309fd96af7f5c3d</fileChecksum>
 </indexedmzML>