diff --git a/tools/msconvert/.shed.yml b/tools/msconvert/.shed.yml
index 70041d931..672328c59 100644
--- a/tools/msconvert/.shed.yml
+++ b/tools/msconvert/.shed.yml
@@ -8,8 +8,7 @@ long_description: |
   Proteowizard msconvert
   Convert and/or filter mass spectrometry files using the offical Docker container.
   Using the Docker container requires agreeing to each vendor's license (for using their proprietary data access libraries): http://www.proteowizard.org/licenses.html
-
-  Main web site: http://www.proteowizard.org
 remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
+homepage_url: http://www.proteowizard.org
 type: unrestricted
 
diff --git a/tools/msconvert/README.md b/tools/msconvert/README.rst
similarity index 100%
rename from tools/msconvert/README.md
rename to tools/msconvert/README.rst
diff --git a/tools/msconvert/msconvert.xml b/tools/msconvert/msconvert.xml
index 054709b77..c74d77d40 100644
--- a/tools/msconvert/msconvert.xml
+++ b/tools/msconvert/msconvert.xml
@@ -1,4 +1,4 @@
-<tool id="msconvert" name="msconvert" version="@VERSION@.2">
+<tool id="msconvert" name="msconvert" version="@VERSION@+galaxy0">
   <description>Convert and/or filter mass spectrometry files</description>
   <macros>
       <import>msconvert_macros.xml</import>
diff --git a/tools/msconvert/msconvert_macros.xml b/tools/msconvert/msconvert_macros.xml
index a5dcc490c..6852f014d 100644
--- a/tools/msconvert/msconvert_macros.xml
+++ b/tools/msconvert/msconvert_macros.xml
@@ -1,6 +1,6 @@
 <macros>
-  <token name="@VERSION@">3.0.20287</token>
-  <token name="@FULL_VERSION@">@VERSION@-769529fa4</token>
+  <token name="@VERSION@">3.0.23187</token>
+  <token name="@FULL_VERSION@">@VERSION@-2243781</token>
   <xml name="msconvertCommand">
     <command detect_errors="exit_code">
 <![CDATA[
@@ -32,7 +32,7 @@
       #set inputmask = "'"+$basename+"'"
     #end if
 
-    #if $data_processing.precursor_refinement.use_mzrefinement
+    #if $data_processing.precursor_refinement.use_mzrefinement == "true"
       #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
       #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
       ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
@@ -61,11 +61,11 @@
     $general_options.acceptZeroLengthSpectra
     $general_options.ignoreUnknownInstrumentError
 
-    #if $general_options.scan_summing.do_scan_summing:
+    #if $general_options.scan_summing.do_scan_summing == "true":
       --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"
     #end if
 
-    #if $general_options.multi_run_output.do_multi_run_output:
+    #if $general_options.multi_run_output.do_multi_run_output == "true":
       #if len($general_options.multi_run_output.run_index_set) > 0
         --runIndexSet "
         #for $index in $general_options.multi_run_output.run_index_set
@@ -81,11 +81,11 @@
     --stripLocationFromSourceFiles
 
     ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
-      #if $data_processing.peak_picking.pick_peaks
+      #if $data_processing.peak_picking.pick_peaks == "true"
         --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
       #end if
 
-      #if $data_processing.precursor_refinement.use_mzrefinement
+      #if $data_processing.precursor_refinement.use_mzrefinement == "true"
       --filter "mzRefiner $input_ident_name
         msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
         thresholdScore=$data_processing.precursor_refinement.thresholdScore
@@ -116,11 +116,11 @@
         --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
       #end for
 
-      #if $data_processing.filter_mz_windows.do_mzwindow_filter
+      #if $data_processing.filter_mz_windows.do_mzwindow_filter == "true"
         --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
       #end if
 
-      #if $data_processing.etd_filtering.do_etd_filtering
+      #if $data_processing.etd_filtering.do_etd_filtering == "true"
         --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
           $data_processing.etd_filtering.remove_charge_reduced
           $data_processing.etd_filtering.remove_neutral_loss
@@ -128,7 +128,7 @@
           $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units"
       #end if
 
-      #if $data_processing.ms2denoise.denoise
+      #if $data_processing.ms2denoise.denoise == "true"
         --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
       #end if
 
@@ -136,7 +136,7 @@
         --filter "MS2Deisotope"
       #end if
 
-      #if $data_processing.demultiplex.demultiplex_on
+      #if $data_processing.demultiplex.demultiplex_on == "true"
         --filter "demultiplex massError=$data_processing.demultiplex.massError$data_processing.demultiplex.massErrorUnits nnlsMaxIter=$data_processing.demultiplex.nnlsMaxIter nnlsEps=$data_processing.demultiplex.nnlsEps noWeighting=$data_processing.demultiplex.noWeighting demuxBlockExtra=$data_processing.demultiplex.demuxBlockExtra variableFill=$data_processing.demultiplex.variableFill noSumNormalize=$data_processing.demultiplex.noSumNormalize optimization=$data_processing.demultiplex.optimization interpolateRT=$data_processing.demultiplex.interpolateRT minWindowSize=$data_processing.demultiplex.minWindowSize"
       #end if
 
@@ -165,7 +165,7 @@
          --filter "stripIT"
       #end if
 
-      #if $filtering.filter_ms_levels.do_ms_level_filter
+      #if $filtering.filter_ms_levels.do_ms_level_filter == "true"
         --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
       #end if
 
@@ -229,7 +229,7 @@
         #end if
       #end if
 
-      #if $data_processing.precursor_refinement.use_mzrefinement
+      #if $data_processing.precursor_refinement.use_mzrefinement == "true"
         && mv '$output_refinement_name' '$output_refinement';
       #end if
 ]]>
@@ -251,7 +251,10 @@
 
     <section name="data_processing" title="Data Processing Filters">
         <conditional name="peak_picking">
-            <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
+            <param type="select" name="pick_peaks" label="Apply peak picking?">
+              <option value="true">Yes</option>
+              <option value="false" selected="true">No</option>
+            </param>
             <when value="false" />
             <when value="true">
                 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
@@ -268,7 +271,10 @@
       </conditional>
 
       <conditional name="precursor_refinement">
-        <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
+        <param type="select" name="use_mzrefinement" label="Apply m/z refinement with identification data?">
+              <option value="true">Yes</option>
+              <option value="false" selected="true">No</option>
+        </param>
         <when value="false"></when>
         <when value="true">
           <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
@@ -337,7 +343,10 @@
       </repeat>
 
       <conditional name="filter_mz_windows">
-        <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
+        <param name="do_mzwindow_filter" type="select" label="Filter m/z Window" help="">
+          <option value="true">Yes</option>
+          <option value="false" selected="true">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
@@ -346,7 +355,10 @@
       </conditional>
 
       <conditional name="etd_filtering">
-        <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
+        <param type="select" name="do_etd_filtering" label="Filter out ETD precursor peaks?">
+          <option value="true">Yes</option>
+          <option value="false" selected="true">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
@@ -374,7 +386,10 @@
       </conditional>
 
       <conditional name="ms2denoise">
-        <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter"  />
+        <param name="denoise" type="select" label="De-noise MS2 with moving window filter">
+          <option value="true">Yes</option>
+          <option value="false" selected="true">No</option>
+        </param>
         <when value="true">
           <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
           <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
@@ -386,7 +401,10 @@
       <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
 
       <conditional name="demultiplex">
-        <param name="demultiplex_on" type="boolean" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)" />
+        <param name="demultiplex_on" type="select" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)" >
+          <option value="true">Yes</option>
+          <option value="false" selected="true">No</option>
+        </param>
         <when value="true">
           <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" />
           <param name="massErrorUnits" type="select" label="Units for Demultiplex Mass Tolerance">
@@ -443,7 +461,10 @@
       <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
 
       <conditional name="filter_ms_levels">
-        <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
+        <param name="do_ms_level_filter" type="select" label="Filter MS Levels">
+          <option value="true">Yes</option>
+          <option value="false" selected="true">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
@@ -471,7 +492,10 @@
       <param argument="--combineIonMobilitySpectra" type="boolean" truevalue="--combineIonMobilitySpectra" falsevalue="" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." />
 
       <conditional name="scan_summing">
-        <param name="do_scan_summing" type="boolean" truevalue="true" falsevalue="false" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR" />
+        <param name="do_scan_summing" type="select" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR">
+          <option value="true">Yes</option>
+          <option value="false" selected="true">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="precursorTol" type="float" label="Precursor m/z tolerance" value="0.05" min="0" optional="true" help="Spectra with precursor m/z values with a difference less than this tolerance are summed together." />
@@ -486,7 +510,10 @@
       <param argument="--ignoreUnknownInstrumentError" type="boolean" truevalue="--ignoreUnknownInstrumentError" falsevalue=""  label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" />
 
       <conditional name="multi_run_output">
-        <param name="do_multi_run_output" type="boolean" truevalue="true" falsevalue="false" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)" />
+        <param name="do_multi_run_output" type="select" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)">
+          <option value="true">Yes</option>
+          <option value="false" selected="true">No</option>
+        </param>
         <when value="false">
           <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" />
         </when>
@@ -523,8 +550,8 @@
 
   <xml name="msconvertOutput">
     <outputs>
-      <data format="mzml" name="output" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}" >
-        <filter>general_options['multi_run_output']['do_multi_run_output'] == False</filter>
+      <data format="mzml" name="output" label="${tool.name} on ${on_string}" >
+        <filter>general_options['multi_run_output']['do_multi_run_output'] == 'false'</filter>
         <change_format>
           <when input="output_type" value="mz5" format="mz5" />
           <when input="output_type" value="mzXML" format="mzxml" />
@@ -532,11 +559,11 @@
           <when input="output_type" value="mgf" format="mgf" />
         </change_format>
       </data>
-      <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv">
-        <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
+      <data format="tsv" name="output_refinement" label="${tool.name} on ${on_string}: mzRefinement">
+        <filter>data_processing['precursor_refinement']['use_mzrefinement'] == 'true'</filter>
       </data>
-      <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}">
-        <filter>general_options['multi_run_output']['do_multi_run_output'] == True</filter>
+      <collection name="multi_run_output_list" type="list" label="${tool.name} on ${on_string}: runs">
+        <filter>general_options['multi_run_output']['do_multi_run_output'] == 'true'</filter>
         <discover_datasets pattern="__name_and_ext__" directory="outputs" />
       </collection>
     </outputs>
@@ -544,7 +571,8 @@
 
 
   <xml name="msconvert_tests">
-    <test>
+    <!-- 1 -->
+    <test expect_num_outputs="1">
       <param name="input" value="small.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -553,7 +581,7 @@
       <param name="pick_peaks_ms_levels" value="1-" />
       <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small.RAW" ftype="thermo.raw" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -562,7 +590,7 @@
       <param name="pick_peaks_ms_levels" value="1-" />
       <output name="output" file="small-peakpicking-vendor-allMS.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.d.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -570,19 +598,20 @@
       <param name="do_scan_summing" value="true" />
       <output name="output" file="ThyroglobMRM000003.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
       <output name="output" file="MassLynxTest.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <!-- 5 -->
+    <test expect_num_outputs="1">
       <param name="input" value="AgilentMassHunterTest.d.tar" ftype="agilentmasshunter.d.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
       <output name="output" file="AgilentMassHunterTest.mzXML" ftype="mzxml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.d.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -599,7 +628,7 @@
       <param name="runIndexSet" value="0" />
       <output name="output" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
@@ -610,7 +639,7 @@
       <param name="srmAsSpectra" value="true" />
       <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
@@ -621,7 +650,8 @@
       <param name="srmAsSpectra" value="true" />
       <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
     </test>
-    <test>
+    <!-- 10 -->
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -633,7 +663,7 @@
         <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
       </output_collection>
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -644,17 +674,17 @@
       </output_collection>
     </test>
 
-    <!-- this data file only has profile MS1, so the result is the same -->
-    <test>
+    <!-- this data file only has profile MS1, so the result is the same (but the file is still quite different because the offsets of the index change) -->
+    <test expect_num_outputs="1">
       <param name="input" value="small.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
       <param name="pick_peaks" value="true" />
       <param name="pick_peaks_algorithm" value="cwt" />
       <param name="pick_peaks_ms_levels" value="1" />
-      <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
+      <output name="output" file="small-peakpicking-cwt-MS1.mzML" ftype="mzml" lines_diff="8" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mz5" />
@@ -662,7 +692,7 @@
       <param name="intensity_encoding" value="64" />
       <output name="output" file="small-zlib-64.mz5" compare="sim_size" ftype="mz5" delta="150000" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
@@ -671,7 +701,7 @@
       <output name="output" file="small-zlib-32.mzXML" ftype="mzxml" lines_diff="6" />
     </test>
     <!-- TODO: how to test gzipped output?
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
       <param name="output_type" value="mzXML" />
       <param name="mz_encoding" value="32" />
@@ -680,7 +710,7 @@
       <param name="gzip_compression" value="true" />
       <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
       <param name="output_type" value="mzML" />
       <param name="mz_encoding" value="32" />
@@ -690,7 +720,7 @@
       <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
     </test>-->
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -698,7 +728,7 @@
       <output name="output" file="small-numpressLP.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -706,7 +736,7 @@
       <output name="output" file="small-numpressLS.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -714,7 +744,7 @@
       <output name="output" file="small-numpressL.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -722,7 +752,7 @@
       <output name="output" file="small-numpressP.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -730,7 +760,7 @@
       <output name="output" file="small-numpressS.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="2">
       <param name="input" value="Rpal_01.mz5" ftype="mz5" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -743,7 +773,7 @@
       <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -756,7 +786,7 @@
       <param name="maxKnownCharge" value="8" />
       <output name="output" file="small-chargeStatePredictor.mzML" ftype="mzml" lines_diff="114" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -771,7 +801,7 @@
       <param name="defaultMaxCharge" value="5" />
       <output name="output" file="small-turbocharger.mzML" ftype="mzml" lines_diff="114" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -785,7 +815,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -798,7 +828,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-threshold.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -808,7 +838,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-mzWindow.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -819,7 +849,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-denoise.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -827,7 +857,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-deisotope.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -835,7 +865,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -848,7 +878,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-index-filter.mzML" lines_diff="32" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -856,7 +886,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-strip-it.mzML" lines_diff="100" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -866,7 +896,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -874,7 +904,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -882,7 +912,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
diff --git a/tools/msconvert/test-data/AgilentMassHunterTest.mzXML b/tools/msconvert/test-data/AgilentMassHunterTest.mzXML
index 2b9a11fe6..a5ad1dbbb 100644
--- a/tools/msconvert/test-data/AgilentMassHunterTest.mzXML
+++ b/tools/msconvert/test-data/AgilentMassHunterTest.mzXML
@@ -2,7 +2,7 @@
 <mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2"
        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
        xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">
-  <msRun scanCount="212" startTime="PT0.668S" endTime="PT209.708S">
+  <msRun scanCount="731" startTime="PT0.668S" endTime="PT207.32S">
     <msInstrument msInstrumentID="1">
       <msManufacturer category="msManufacturer" value="instrument model"/>
       <msModel category="msModel" value="Agilent instrument model"/>
@@ -12,7 +12,7 @@
       <software type="acquisition" name="MassHunter Data Acquisition" version="8.0"/>
     </msInstrument>
     <dataProcessing>
-      <software type="conversion" name="ProteoWizard software" version="3.0.20287"/>
+      <software type="conversion" name="ProteoWizard software" version="3.0.23187"/>
       <processingOperation name="Conversion to mzML"/>
     </dataProcessing>
     <scan num="676"
@@ -25,8 +25,8 @@
           lowMz="101.059547842973"
           highMz="961.958412367698"
           basePeakMz="622.030137146612"
-          basePeakIntensity="69123.5234"
-          totIonCurrent="248205.188"
+          basePeakIntensity="69123.52344"
+          totIonCurrent="2.48205e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="2042"
@@ -45,7 +45,7 @@
           highMz="960.969890733779"
           basePeakMz="622.030314834219"
           basePeakIntensity="66012.125"
-          totIonCurrent="242169.563"
+          totIonCurrent="2.4217e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1910"
@@ -63,8 +63,8 @@
           lowMz="101.059622428728"
           highMz="960.974437956773"
           basePeakMz="622.03039195514"
-          basePeakIntensity="66470.3359"
-          totIonCurrent="235904.875"
+          basePeakIntensity="66470.33594"
+          totIonCurrent="2.35905e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1843"
@@ -82,8 +82,8 @@
           lowMz="101.058794580356"
           highMz="960.961063835533"
           basePeakMz="622.030204388004"
-          basePeakIntensity="66440.2656"
-          totIonCurrent="232857.063"
+          basePeakIntensity="66440.26563"
+          totIonCurrent="2.32857e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1777"
@@ -101,8 +101,8 @@
           lowMz="101.058861963583"
           highMz="960.955505659212"
           basePeakMz="622.030101649123"
-          basePeakIntensity="66296.9688"
-          totIonCurrent="237769.328"
+          basePeakIntensity="66296.96875"
+          totIonCurrent="2.37769e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1911"
@@ -120,8 +120,8 @@
           lowMz="101.059907560808"
           highMz="961.959504148079"
           basePeakMz="622.030635031507"
-          basePeakIntensity="66336.8203"
-          totIonCurrent="231152.781"
+          basePeakIntensity="66336.82031"
+          totIonCurrent="2.31153e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1684"
@@ -139,8 +139,8 @@
           lowMz="101.059912905858"
           highMz="960.971032543987"
           basePeakMz="622.030388026695"
-          basePeakIntensity="66918.0547"
-          totIonCurrent="240991.938"
+          basePeakIntensity="66918.05469"
+          totIonCurrent="2.40992e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1955"
@@ -158,8 +158,8 @@
           lowMz="101.059044861993"
           highMz="961.950855756299"
           basePeakMz="622.030809786758"
-          basePeakIntensity="66243.5938"
-          totIonCurrent="238295.063"
+          basePeakIntensity="66243.59375"
+          totIonCurrent="2.38295e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1892"
@@ -178,7 +178,7 @@
           highMz="961.963102411637"
           basePeakMz="622.030473502298"
           basePeakIntensity="68151.9375"
-          totIonCurrent="238181.078"
+          totIonCurrent="2.38181e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1822"
@@ -197,7 +197,7 @@
           highMz="960.962465448603"
           basePeakMz="622.029978679818"
           basePeakIntensity="67345.375"
-          totIonCurrent="246848.297"
+          totIonCurrent="2.46848e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1868"
@@ -215,8 +215,8 @@
           lowMz="101.060477112231"
           highMz="960.957167113979"
           basePeakMz="622.029829994687"
-          basePeakIntensity="68870.6484"
-          totIonCurrent="241214.25"
+          basePeakIntensity="68870.64844"
+          totIonCurrent="2.41214e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1749"
@@ -234,8 +234,8 @@
           lowMz="101.059811320755"
           highMz="960.96023124854"
           basePeakMz="622.030151010764"
-          basePeakIntensity="68875.0938"
-          totIonCurrent="245569.859"
+          basePeakIntensity="68875.09375"
+          totIonCurrent="2.4557e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1902"
@@ -253,8 +253,8 @@
           lowMz="101.05964870704"
           highMz="960.956366764158"
           basePeakMz="622.030682680831"
-          basePeakIntensity="69098.4922"
-          totIonCurrent="246561.859"
+          basePeakIntensity="69098.49219"
+          totIonCurrent="2.46562e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="2029"
@@ -272,8 +272,8 @@
           lowMz="101.059384850868"
           highMz="960.956623221231"
           basePeakMz="622.030554131862"
-          basePeakIntensity="66741.5156"
-          totIonCurrent="247536.516"
+          basePeakIntensity="66741.51563"
+          totIonCurrent="2.47537e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1973"
@@ -291,8 +291,8 @@
           lowMz="101.059363744759"
           highMz="960.956993401452"
           basePeakMz="622.031252265985"
-          basePeakIntensity="68359.2031"
-          totIonCurrent="244628.922"
+          basePeakIntensity="68359.20313"
+          totIonCurrent="2.44629e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1978"
@@ -310,8 +310,8 @@
           lowMz="101.059387586902"
           highMz="960.969305455936"
           basePeakMz="622.030058834573"
-          basePeakIntensity="69184.7031"
-          totIonCurrent="247788.469"
+          basePeakIntensity="69184.70313"
+          totIonCurrent="2.47788e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1981"
@@ -329,8 +329,8 @@
           lowMz="101.059756727983"
           highMz="960.957929091948"
           basePeakMz="622.029963943234"
-          basePeakIntensity="69327.4141"
-          totIonCurrent="248146.969"
+          basePeakIntensity="69327.41406"
+          totIonCurrent="2.48147e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1868"
@@ -348,8 +348,8 @@
           lowMz="101.059730855593"
           highMz="960.958714366903"
           basePeakMz="622.029898604064"
-          basePeakIntensity="68995.2969"
-          totIonCurrent="244799.813"
+          basePeakIntensity="68995.29688"
+          totIonCurrent="2.448e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1855"
@@ -368,7 +368,7 @@
           highMz="960.961251634941"
           basePeakMz="622.030149104179"
           basePeakIntensity="69121.5"
-          totIonCurrent="252602.641"
+          totIonCurrent="2.52603e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="2078"
@@ -386,8 +386,8 @@
           lowMz="100.112271961642"
           highMz="960.962373322871"
           basePeakMz="622.030131302134"
-          basePeakIntensity="70879.6953"
-          totIonCurrent="246828.938"
+          basePeakIntensity="70879.69531"
+          totIonCurrent="2.46829e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1856"
@@ -405,8 +405,8 @@
           lowMz="100.111900175635"
           highMz="961.951277883158"
           basePeakMz="622.030367329583"
-          basePeakIntensity="70043.9531"
-          totIonCurrent="255779.563"
+          basePeakIntensity="70043.95313"
+          totIonCurrent="2.5578e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="2043"
@@ -424,8 +424,8 @@
           lowMz="101.059113525667"
           highMz="960.958141647057"
           basePeakMz="622.030220786266"
-          basePeakIntensity="71269.7969"
-          totIonCurrent="249458.563"
+          basePeakIntensity="71269.79688"
+          totIonCurrent="2.49459e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1890"
@@ -444,7 +444,7 @@
           highMz="960.968538524987"
           basePeakMz="622.031005097876"
           basePeakIntensity="70687.1875"
-          totIonCurrent="251625.75"
+          totIonCurrent="2.51626e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="2056"
@@ -462,8 +462,8 @@
           lowMz="101.058766625423"
           highMz="960.962155896741"
           basePeakMz="622.031095439861"
-          basePeakIntensity="71181.5469"
-          totIonCurrent="251850.594"
+          basePeakIntensity="71181.54688"
+          totIonCurrent="2.51851e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1964"
@@ -481,8 +481,8 @@
           lowMz="101.059479965957"
           highMz="960.957078485954"
           basePeakMz="622.030667482374"
-          basePeakIntensity="70054.4844"
-          totIonCurrent="252991.063"
+          basePeakIntensity="70054.48438"
+          totIonCurrent="2.52991e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1998"
@@ -500,8 +500,8 @@
           lowMz="101.059560221832"
           highMz="960.96169274376"
           basePeakMz="622.031822900269"
-          basePeakIntensity="67961.6797"
-          totIonCurrent="247450.516"
+          basePeakIntensity="67961.67969"
+          totIonCurrent="2.47451e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1902"
@@ -519,8 +519,8 @@
           lowMz="101.059988697105"
           highMz="960.962355184896"
           basePeakMz="622.031605315467"
-          basePeakIntensity="66246.3281"
-          totIonCurrent="241074.766"
+          basePeakIntensity="66246.32813"
+          totIonCurrent="2.41075e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1922"
@@ -538,8 +538,8 @@
           lowMz="101.059193080831"
           highMz="961.959963271624"
           basePeakMz="622.031324985045"
-          basePeakIntensity="62883.0859"
-          totIonCurrent="224256.047"
+          basePeakIntensity="62883.08594"
+          totIonCurrent="2.24256e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1749"
@@ -557,8 +557,8 @@
           lowMz="101.059543236014"
           highMz="961.960523658431"
           basePeakMz="622.031407174498"
-          basePeakIntensity="64459.2266"
-          totIonCurrent="214464.844"
+          basePeakIntensity="64459.22656"
+          totIonCurrent="2.14465e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1645"
@@ -576,8 +576,8 @@
           lowMz="101.059668584602"
           highMz="961.955002886972"
           basePeakMz="622.03137975999"
-          basePeakIntensity="61906.7109"
-          totIonCurrent="216728.781"
+          basePeakIntensity="61906.71094"
+          totIonCurrent="2.16729e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1722"
@@ -595,8 +595,8 @@
           lowMz="101.060037876524"
           highMz="960.965631367469"
           basePeakMz="622.030485484062"
-          basePeakIntensity="64743.4141"
-          totIonCurrent="224832.938"
+          basePeakIntensity="64743.41406"
+          totIonCurrent="2.24833e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1731"
@@ -614,8 +614,8 @@
           lowMz="101.059712851925"
           highMz="960.969957839822"
           basePeakMz="622.030153400646"
-          basePeakIntensity="66161.8594"
-          totIonCurrent="227879.969"
+          basePeakIntensity="66161.85938"
+          totIonCurrent="2.2788e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1781"
@@ -633,8 +633,8 @@
           lowMz="101.059405575765"
           highMz="960.962993201507"
           basePeakMz="622.030147177136"
-          basePeakIntensity="66889.7109"
-          totIonCurrent="237125.094"
+          basePeakIntensity="66889.71094"
+          totIonCurrent="2.37125e05"
           msInstrumentID="1">
       <peaks compressionType="zlib"
              compressedLen="1760"
@@ -652,8 +652,8 @@
           lowMz="101.059519842364"
           highMz="960.968029709625"
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-  <indexOffset>689294</indexOffset>
-  <sha1>919d9f6aaa20533cbe9c75398a139a36bec4b6b0</sha1>
+  <indexOffset>1262019</indexOffset>
+  <sha1>90afb85af8a80208632fa0cdda6c81ec4783b591</sha1>
 </mzXML>
diff --git a/tools/msconvert/test-data/BrukerBafTest.mzML b/tools/msconvert/test-data/BrukerBafTest.mzML
index a1891a8f7..2ea4fc5b1 100644
--- a/tools/msconvert/test-data/BrukerBafTest.mzML
+++ b/tools/msconvert/test-data/BrukerBafTest.mzML
@@ -2,7 +2,7 @@
 <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="BrukerBafTest" version="1.1.0">
     <cvList count="2">
-      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -30,7 +30,7 @@
       <software id="apexControl" version="ApexControl 3.0.0.alpha.35 (development version, April 18, 2008)">
         <cvParam cvRef="MS" accession="MS:1000706" name="apexControl" value=""/>
       </software>
-      <software id="pwiz_Reader_Bruker" version="3.0.20287">
+      <software id="pwiz_Reader_Bruker" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -152,13 +152,13 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
-      <offset idRef="scan=1">4264</offset>
+      <offset idRef="scan=1">4265</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">7765</offset>
-      <offset idRef="BPC">9468</offset>
+      <offset idRef="TIC">7766</offset>
+      <offset idRef="BPC">9469</offset>
     </index>
   </indexList>
-  <indexListOffset>11203</indexListOffset>
-  <fileChecksum>913c285a998996d2707f6f242bf7a0c00bd6468b</fileChecksum>
+  <indexListOffset>11204</indexListOffset>
+  <fileChecksum>f4d47401a5d1194ffcc04e2fc3ebbdc15ae2d685</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML b/tools/msconvert/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML
index 8620cf605..5da863f57 100644
--- a/tools/msconvert/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML
+++ b/tools/msconvert/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML
@@ -70,6 +70,7 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;ETDFilter true true false false 50.0PPM&quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile D100930_yeast_SCX10S_rak_ft8E_pc_01"/>
         </processingMethod>
         <processingMethod order="1" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1001486" name="data filtering" value=""/>
@@ -4675,85 +4676,85 @@
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">534001</offset>
+      <offset idRef="TIC">534361</offset>
     </index>
   </indexList>
-  <indexListOffset>603060</indexListOffset>
-  <fileChecksum>d3351c1b6a0323ea6f4aa59884b68a99da6b9b8c</fileChecksum>
+  <indexListOffset>603420</indexListOffset>
+  <fileChecksum>1b726df8637916e6676f332cc68216231fa9d338</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/MassLynxTest.mzML b/tools/msconvert/test-data/MassLynxTest.mzML
index b4071ffe9..37ace5932 100644
--- a/tools/msconvert/test-data/MassLynxTest.mzML
+++ b/tools/msconvert/test-data/MassLynxTest.mzML
@@ -2,7 +2,7 @@
 <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="MassLynxTest" version="1.1.0">
     <cvList count="2">
-      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -391,7 +391,7 @@
       <software id="MassLynx" version="4.1">
         <cvParam cvRef="MS" accession="MS:1000534" name="MassLynx" value=""/>
       </software>
-      <software id="pwiz_Reader_Waters" version="3.0.20287">
+      <software id="pwiz_Reader_Waters" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -1219,7 +1219,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="418.726013" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="418.72601" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1227,7 +1227,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="666.343323" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="666.34332" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
           </product>
           <binaryDataArrayList count="2">
@@ -1250,7 +1250,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="418.726013" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="418.72601" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1258,7 +1258,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="723.361877" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="723.36188" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
           </product>
           <binaryDataArrayList count="2">
@@ -1281,7 +1281,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="461.745087" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="461.74509" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1289,7 +1289,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="476.260986" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="476.26099" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
           </product>
           <binaryDataArrayList count="2">
@@ -1312,7 +1312,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="461.745087" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="461.74509" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1320,7 +1320,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="722.401428" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="722.40143" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
           </product>
           <binaryDataArrayList count="2">
@@ -1351,7 +1351,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="581.260986" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="581.26099" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
           </product>
           <binaryDataArrayList count="2">
@@ -1382,7 +1382,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="841.415588" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="841.41559" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
           </product>
           <binaryDataArrayList count="2">
@@ -1444,7 +1444,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="951.471375" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="951.47137" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
           </product>
           <binaryDataArrayList count="2">
@@ -1467,7 +1467,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="602.794617" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="602.79462" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1475,7 +1475,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="792.345581" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="792.34558" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
           </product>
           <binaryDataArrayList count="2">
@@ -1498,7 +1498,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="602.794617" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="602.79462" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1506,7 +1506,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="921.387207" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="921.38721" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
           </product>
           <binaryDataArrayList count="2">
@@ -1529,7 +1529,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="618.335999" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="618.336" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1560,7 +1560,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="618.335999" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="618.336" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1591,7 +1591,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="629.836426" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="629.83643" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1599,7 +1599,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="832.436707" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="832.43671" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
           </product>
           <binaryDataArrayList count="2">
@@ -1622,7 +1622,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="629.836426" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="629.83643" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1653,7 +1653,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="643.859985" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="643.85999" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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@@ -1661,7 +1661,7 @@
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-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="745.458374" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="745.45837" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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@@ -1684,7 +1684,7 @@
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-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="643.859985" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="643.85999" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1715,7 +1715,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
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-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="644.861694" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="644.86169" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1723,7 +1723,7 @@
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-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="834.448181" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="834.44818" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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@@ -1746,7 +1746,7 @@
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-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="644.861694" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="644.86169" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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@@ -1777,7 +1777,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
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-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="721.852783" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="721.85278" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1785,7 +1785,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="856.371826" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="856.37183" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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@@ -1808,7 +1808,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="721.852783" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="721.85278" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1839,7 +1839,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="724.406982" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="724.40698" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1847,7 +1847,7 @@
           </precursor>
           <product>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="778.392822" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="778.39282" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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@@ -1870,7 +1870,7 @@
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <precursor>
             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="724.406982" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="724.40698" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
@@ -1909,7 +1909,7 @@
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-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="761.435425" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="761.43542" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
             </isolationWindow>
           </product>
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@@ -1940,7 +1940,7 @@
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             <isolationWindow>
-              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="832.471497" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="832.4715" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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@@ -1963,50 +1963,50 @@
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diff --git a/tools/msconvert/test-data/Rpal_01-mzRefinement.mzML b/tools/msconvert/test-data/Rpal_01-mzRefinement.mzML
index 0f838fdca..4787ef3ff 100644
--- a/tools/msconvert/test-data/Rpal_01-mzRefinement.mzML
+++ b/tools/msconvert/test-data/Rpal_01-mzRefinement.mzML
@@ -70,6 +70,7 @@
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         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="Rpal_01.mz5 --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;mzRefiner Rpal_01.pepxml msLevels=1- thresholdScore=mvh thresholdValue=40- thresholdStep=0.0 maxSteps=0 assumeHighRes=1&quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile Rpal_01"/>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=101">562519</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=102">568172</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">573525</offset>
+      <offset idRef="TIC">573909</offset>
     </index>
   </indexList>
-  <indexListOffset>611925</indexListOffset>
-  <fileChecksum>f6cdf7e6c379dfe7b91b25a6c61099502d6fba3b</fileChecksum>
+  <indexListOffset>612309</indexListOffset>
+  <fileChecksum>5eadb7d9d0c1dc18826c760a222f161d8db608c0</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/SciexTest-HPINalone-NE-srmAsSpectra.mzXML b/tools/msconvert/test-data/SciexTest-HPINalone-NE-srmAsSpectra.mzXML
index d92d7081d..1a6504d0a 100644
--- a/tools/msconvert/test-data/SciexTest-HPINalone-NE-srmAsSpectra.mzXML
+++ b/tools/msconvert/test-data/SciexTest-HPINalone-NE-srmAsSpectra.mzXML
@@ -15,7 +15,7 @@
       <software type="acquisition" name="Analyst" version="unknown"/>
     </msInstrument>
     <dataProcessing>
-      <software type="conversion" name="ProteoWizard software" version="3.0.20287"/>
+      <software type="conversion" name="ProteoWizard software" version="3.0.23187"/>
       <processingOperation name="Conversion to mzML"/>
     </dataProcessing>
     <scan num="1"
@@ -9022,5 +9022,5 @@
     <offset id="500">441024</offset>
   </index>
   <indexOffset>441951</indexOffset>
-  <sha1>53f184f3f70d339f8d1ced50e7edf4b0b3db0867</sha1>
+  <sha1>e3ccd25b6035ba388fee1b820f8f7b2d822f3313</sha1>
 </mzXML>
diff --git a/tools/msconvert/test-data/SciexTest-HPINalone-NE.mzML b/tools/msconvert/test-data/SciexTest-HPINalone-NE.mzML
index 64f5d516a..94147fb9b 100644
--- a/tools/msconvert/test-data/SciexTest-HPINalone-NE.mzML
+++ b/tools/msconvert/test-data/SciexTest-HPINalone-NE.mzML
@@ -2,7 +2,7 @@
 <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="SciexTest-HPINalone+NE" version="1.1.0">
     <cvList count="2">
-      <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="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -26,13 +26,14 @@
       <software id="Analyst" version="unknown">
         <cvParam cvRef="MS" accession="MS:1000551" name="Analyst" value=""/>
       </software>
-      <software id="pwiz_Reader_ABI" version="3.0.19044">
+      <software id="pwiz_Reader_ABI" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
     <instrumentConfigurationList count="1">
       <instrumentConfiguration id="IC1">
         <cvParam cvRef="MS" accession="MS:1000139" name="4000 QTRAP" value=""/>
+        <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="U016980608"/>
         <componentList count="5">
           <source order="1">
             <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
@@ -61,25 +62,54 @@
       </dataProcessing>
     </dataProcessingList>
     <run id="SciexTest-HPINalone_x002b_NE" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2008-12-01T00:19:01Z" defaultSourceFileRef="WIFF">
-      <chromatogramList count="39" defaultDataProcessingRef="pwiz_Reader_ABI_conversion">
-        <chromatogram index="0" id="TIC" defaultArrayLength="2604">
+      <chromatogramList count="40" defaultDataProcessingRef="pwiz_Reader_ABI_conversion">
+        <chromatogram index="0" id="TIC" defaultArrayLength="1353">
           <cvParam cvRef="MS" accession="MS:1000235" name="total ion current chromatogram" value=""/>
-          <binaryDataArrayList count="2">
-            <binaryDataArray encodedLength="17052">
+          <binaryDataArrayList count="3">
+            <binaryDataArray encodedLength="10896">
               <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
               <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
               <cvParam cvRef="MS" accession="MS:1000595" name="time array" value="" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
-              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+              <cvParam cvRef="MS" accession="MS:1000595" name="time array" value="" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
+              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-      <offset idRef="SRM SIC Q1=529.234 Q3=651.246 sample=2 period=1 experiment=1 transition=29">440632</offset>
-      <offset idRef="SRM SIC Q1=529.234 Q3=832.276 sample=2 period=1 experiment=1 transition=30">454884</offset>
-      <offset idRef="SRM SIC Q1=529.234 Q3=945.36 sample=2 period=1 experiment=1 transition=31">469232</offset>
-      <offset idRef="SRM SIC Q1=529.234 Q3=470.217 sample=2 period=1 experiment=1 transition=32">483595</offset>
-      <offset idRef="SRM SIC Q1=713.355 Q3=838.459 sample=2 period=1 experiment=1 transition=33">498202</offset>
-      <offset idRef="SRM SIC Q1=713.355 Q3=1200.52 sample=2 period=1 experiment=1 transition=34">512209</offset>
-      <offset idRef="SRM SIC Q1=713.355 Q3=657.43 sample=2 period=1 experiment=1 transition=35">526225</offset>
-      <offset idRef="SRM SIC Q1=475.906 Q3=544.346 sample=2 period=1 experiment=1 transition=36">540564</offset>
-      <offset idRef="SRM SIC Q1=475.906 Q3=657.43 sample=2 period=1 experiment=1 transition=37">555003</offset>
+      <offset idRef="TIC">4009</offset>
+      <offset idRef="BPC">20091</offset>
+      <offset idRef="SRM SIC Q1=264.114 Q3=396.129 sample=2 period=1 experiment=1 transition=0 ce=13.9698 name=H-PIN1_264.11_396.12865">35648</offset>
+      <offset idRef="SRM SIC Q1=264.114 Q3=395.204 sample=2 period=1 experiment=1 transition=1 ce=13.9698 name=H-PIN1_264.11_395.20429">49701</offset>
+      <offset idRef="SRM SIC Q1=477.198 Q3=345.145 sample=2 period=1 experiment=1 transition=2 ce=26.4967 name=H-PIN2_477.2_345.14505">64107</offset>
+      <offset idRef="SRM SIC Q1=318.468 Q3=345.145 sample=2 period=1 experiment=1 transition=3 ce=16.7419 name=H-PIN2_318.47_345.14505">78624</offset>
+      <offset idRef="SRM SIC Q1=318.468 Q3=501.246 sample=2 period=1 experiment=1 transition=4 ce=16.7419 name=H-PIN2_318.47_501.24616">92592</offset>
+      <offset idRef="SRM SIC Q1=318.468 Q3=558.268 sample=2 period=1 experiment=1 transition=5 ce=16.7419 name=H-PIN2_318.47_558.26762">106252</offset>
+      <offset idRef="SRM SIC Q1=526.732 Q3=477.15 sample=2 period=1 experiment=1 transition=6 ce=28.6762 name=H-PIN3_526.73_477.15">120328</offset>
+      <offset idRef="SRM SIC Q1=351.491 Q3=396.129 sample=2 period=1 experiment=1 transition=7 ce=18.426 name=H-PIN3_351.49_396.12865">134912</offset>
+      <offset idRef="SRM SIC Q1=351.491 Q3=772.315 sample=2 period=1 experiment=1 transition=8 ce=18.426 name=H-PIN3_351.49_772.31455">149272</offset>
+      <offset idRef="SRM SIC Q1=526.732 Q3=657.336 sample=2 period=1 experiment=1 transition=9 ce=28.6762 name=H-PIN3_526.73_657.33603">162872</offset>
+      <offset idRef="SRM SIC Q1=351.491 Q3=281.15 sample=2 period=1 experiment=1 transition=10 ce=18.426 name=H-PIN3_351.49_281.15013">176914</offset>
+      <offset idRef="SRM SIC Q1=608.264 Q3=820.399 sample=2 period=1 experiment=1 transition=11 ce=32.2636 name=H-PIN4_608.26_820.39936">191175</offset>
+      <offset idRef="SRM SIC Q1=405.845 Q3=607.277 sample=2 period=1 experiment=1 transition=12 ce=21.1981 name=H-PIN4_405.85_607.27679">205033</offset>
+      <offset idRef="SRM SIC Q1=405.845 Q3=820.399 sample=2 period=1 experiment=1 transition=13 ce=21.1981 name=H-PIN4_405.85_820.39936">218996</offset>
+      <offset idRef="SRM SIC Q1=405.845 Q3=281.15 sample=2 period=1 experiment=1 transition=14 ce=21.1981 name=H-PIN4_405.85_281.15013">232531</offset>
+      <offset idRef="SRM SIC Q1=541.221 Q3=318.112 sample=2 period=1 experiment=1 transition=15 ce=29.3137 name=H-PIN5_541.22_318.112157">246966</offset>
+      <offset idRef="SRM SIC Q1=361.15 Q3=499.142 sample=2 period=1 experiment=1 transition=16 ce=18.9187 name=H-PIN5_361.15_499.141595">261359</offset>
+      <offset idRef="SRM SIC Q1=541.221 Q3=583.301 sample=2 period=1 experiment=1 transition=17 ce=29.3137 name=H-PIN5_541.22_583.301068">275354</offset>
+      <offset idRef="SRM SIC Q1=541.221 Q3=764.331 sample=2 period=1 experiment=1 transition=18 ce=29.3137 name=H-PIN5_541.22_764.330506">289643</offset>
+      <offset idRef="SRM SIC Q1=541.221 Q3=945.36 sample=2 period=1 experiment=1 transition=19 ce=29.3137 name=H-PIN5_541.22_945.359944">303932</offset>
+      <offset idRef="SRM SIC Q1=361.15 Q3=260.197 sample=2 period=1 experiment=1 transition=20 ce=18.9187 name=H-PIN5_361.15_260.19741">318228</offset>
+      <offset idRef="SRM SIC Q1=345.113 Q3=259.16 sample=2 period=1 experiment=1 transition=21 ce=20.685 name=H-PIN6_345.11_259.16">333059</offset>
+      <offset idRef="SRM SIC Q1=345.113 Q3=509.172 sample=2 period=1 experiment=1 transition=22 ce=20.685 name=H-PIN6_345.11_509.172226">347539</offset>
+      <offset idRef="SRM SIC Q1=487.187 Q3=541.254 sample=2 period=1 experiment=1 transition=23 ce=26.9362 name=H-PIN7_487.19_541.254118">361806</offset>
+      <offset idRef="SRM SIC Q1=487.187 Q3=722.284 sample=2 period=1 experiment=1 transition=24 ce=26.9362 name=H-PIN7_487.19_722.283556">376334</offset>
+      <offset idRef="SRM SIC Q1=487.187 Q3=903.313 sample=2 period=1 experiment=1 transition=25 ce=26.9362 name=H-PIN7_487.19_903.312994">390650</offset>
+      <offset idRef="SRM SIC Q1=487.187 Q3=360.225 sample=2 period=1 experiment=1 transition=26 ce=26.9362 name=H-PIN7_487.19_360.22468">404532</offset>
+      <offset idRef="SRM SIC Q1=529.234 Q3=185.1 sample=2 period=1 experiment=1 transition=27 ce=28.7863 name=H-PIN8_529.23_185.1">419219</offset>
+      <offset idRef="SRM SIC Q1=529.234 Q3=477.15 sample=2 period=1 experiment=1 transition=28 ce=28.7863 name=H-PIN8_529.23_477.15">434382</offset>
+      <offset idRef="SRM SIC Q1=529.234 Q3=651.246 sample=2 period=1 experiment=1 transition=29 ce=28.7863 name=H-PIN8_529.23_651.246446">448960</offset>
+      <offset idRef="SRM SIC Q1=529.234 Q3=832.276 sample=2 period=1 experiment=1 transition=30 ce=28.7863 name=H-PIN8_529.23_832.275884">463265</offset>
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+      <offset idRef="SRM SIC Q1=529.234 Q3=470.217 sample=2 period=1 experiment=1 transition=32 ce=28.7863 name=H-PIN8_529.23_470.217008">492082</offset>
+      <offset idRef="SRM SIC Q1=713.355 Q3=838.459 sample=2 period=1 experiment=1 transition=33 ce=36.8876 name=H-PIN9_713.36_838.459348">506742</offset>
+      <offset idRef="SRM SIC Q1=713.355 Q3=1200.52 sample=2 period=1 experiment=1 transition=34 ce=36.8876 name=H-PIN9_713.36_1200.518224">520802</offset>
+      <offset idRef="SRM SIC Q1=713.355 Q3=657.43 sample=2 period=1 experiment=1 transition=35 ce=36.8876 name=H-PIN9_713.36_657.42991">534872</offset>
+      <offset idRef="SRM SIC Q1=475.906 Q3=544.346 sample=2 period=1 experiment=1 transition=36 ce=24.7712 name=H-PIN9_475.91_544.34585">549263</offset>
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     </index>
   </indexList>
-  <indexListOffset>569474</indexListOffset>
-  <fileChecksum>89c00bdd35cabd8f18a0f965830b5f5ed9d9bc24</fileChecksum>
+  <indexListOffset>578273</indexListOffset>
+  <fileChecksum>32ae2807934a3b38e6f36efa9ba0e3e0c4deef4b</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/SciexTest-HPINalone-srmAsSpectra.mzXML b/tools/msconvert/test-data/SciexTest-HPINalone-srmAsSpectra.mzXML
index 98d97624e..d246a5118 100644
--- a/tools/msconvert/test-data/SciexTest-HPINalone-srmAsSpectra.mzXML
+++ b/tools/msconvert/test-data/SciexTest-HPINalone-srmAsSpectra.mzXML
@@ -15,7 +15,7 @@
       <software type="acquisition" name="Analyst" version="unknown"/>
     </msInstrument>
     <dataProcessing>
-      <software type="conversion" name="ProteoWizard software" version="3.0.20287"/>
+      <software type="conversion" name="ProteoWizard software" version="3.0.23187"/>
       <processingOperation name="Conversion to mzML"/>
     </dataProcessing>
     <scan num="1"
@@ -9022,5 +9022,5 @@
     <offset id="500">436738</offset>
   </index>
   <indexOffset>437632</indexOffset>
-  <sha1>5bfe9815b1cad4c396b0eb186fc4035f10664d16</sha1>
+  <sha1>962aea2365ad1ee1031627c9171055fea0360adc</sha1>
 </mzXML>
diff --git a/tools/msconvert/test-data/SciexTest-HPINalone.mzML b/tools/msconvert/test-data/SciexTest-HPINalone.mzML
index ac9ad816a..4272c795c 100644
--- a/tools/msconvert/test-data/SciexTest-HPINalone.mzML
+++ b/tools/msconvert/test-data/SciexTest-HPINalone.mzML
@@ -2,7 +2,7 @@
 <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="SciexTest-HPINalone" version="1.1.0">
     <cvList count="2">
-      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -26,7 +26,7 @@
       <software id="Analyst" version="unknown">
         <cvParam cvRef="MS" accession="MS:1000551" name="Analyst" value=""/>
       </software>
-      <software id="pwiz_Reader_ABI" version="3.0.20287">
+      <software id="pwiz_Reader_ABI" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -78,11 +78,11 @@
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-            <binaryDataArray arrayLength="1353" encodedLength="44">
+            <binaryDataArray arrayLength="1353" encodedLength="56">
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               <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
               <cvParam cvRef="MS" accession="MS:1000786" name="non-standard data array" value="ms level" unitCvRef="UO" unitAccession="UO:0000186" unitName="dimensionless unit"/>
-              <binary>eJztwQEBAAAAgiD/r25IQAEAAAAAAAAAAADwaCpIAAE=</binary>
+              <binary>eJztxTEBAAAMAqDZv/QOYwgPuYpt27Zt27Zt27Zt27Zt27anfgFABUo=</binary>
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-              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="0.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
+              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="28.786291122437" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
             </activation>
           </precursor>
           <product>
@@ -1165,7 +1165,7 @@
             </binaryDataArray>
           </binaryDataArrayList>
         </chromatogram>
-        <chromatogram index="34" id="SRM SIC Q1=529.234 Q3=470.217 sample=1 period=1 experiment=1 transition=32" defaultArrayLength="1353">
+        <chromatogram index="34" id="SRM SIC Q1=529.234 Q3=470.217 sample=1 period=1 experiment=1 transition=32 ce=28.7863 name=H-PIN8_529.23_470.217008" defaultArrayLength="1353">
           <cvParam cvRef="MS" accession="MS:1001473" name="selected reaction monitoring chromatogram" value=""/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <userParam name="MS_dwell_time" value="0.10000000000000001" type="xs:float"/>
@@ -1175,7 +1175,7 @@
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
-              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="0.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
+              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="28.786291122437" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
             </activation>
           </precursor>
           <product>
@@ -1198,7 +1198,7 @@
             </binaryDataArray>
           </binaryDataArrayList>
         </chromatogram>
-        <chromatogram index="35" id="SRM SIC Q1=713.355 Q3=838.459 sample=1 period=1 experiment=1 transition=33" defaultArrayLength="1353">
+        <chromatogram index="35" id="SRM SIC Q1=713.355 Q3=838.459 sample=1 period=1 experiment=1 transition=33 ce=36.8876 name=H-PIN9_713.36_838.459348" defaultArrayLength="1353">
           <cvParam cvRef="MS" accession="MS:1001473" name="selected reaction monitoring chromatogram" value=""/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <userParam name="MS_dwell_time" value="0.10000000000000001" type="xs:float"/>
@@ -1208,7 +1208,7 @@
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
-              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="0.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
+              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="36.887622833252" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
             </activation>
           </precursor>
           <product>
@@ -1231,7 +1231,7 @@
             </binaryDataArray>
           </binaryDataArrayList>
         </chromatogram>
-        <chromatogram index="36" id="SRM SIC Q1=713.355 Q3=1200.52 sample=1 period=1 experiment=1 transition=34" defaultArrayLength="1353">
+        <chromatogram index="36" id="SRM SIC Q1=713.355 Q3=1200.52 sample=1 period=1 experiment=1 transition=34 ce=36.8876 name=H-PIN9_713.36_1200.518224" defaultArrayLength="1353">
           <cvParam cvRef="MS" accession="MS:1001473" name="selected reaction monitoring chromatogram" value=""/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <userParam name="MS_dwell_time" value="0.10000000000000001" type="xs:float"/>
@@ -1241,7 +1241,7 @@
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
-              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="0.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
+              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="36.887622833252" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
             </activation>
           </precursor>
           <product>
@@ -1264,7 +1264,7 @@
             </binaryDataArray>
           </binaryDataArrayList>
         </chromatogram>
-        <chromatogram index="37" id="SRM SIC Q1=713.355 Q3=657.43 sample=1 period=1 experiment=1 transition=35" defaultArrayLength="1353">
+        <chromatogram index="37" id="SRM SIC Q1=713.355 Q3=657.43 sample=1 period=1 experiment=1 transition=35 ce=36.8876 name=H-PIN9_713.36_657.42991" defaultArrayLength="1353">
           <cvParam cvRef="MS" accession="MS:1001473" name="selected reaction monitoring chromatogram" value=""/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <userParam name="MS_dwell_time" value="0.10000000000000001" type="xs:float"/>
@@ -1274,7 +1274,7 @@
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
-              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="0.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
+              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="36.887622833252" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
             </activation>
           </precursor>
           <product>
@@ -1297,7 +1297,7 @@
             </binaryDataArray>
           </binaryDataArrayList>
         </chromatogram>
-        <chromatogram index="38" id="SRM SIC Q1=475.906 Q3=544.346 sample=1 period=1 experiment=1 transition=36" defaultArrayLength="1353">
+        <chromatogram index="38" id="SRM SIC Q1=475.906 Q3=544.346 sample=1 period=1 experiment=1 transition=36 ce=24.7712 name=H-PIN9_475.91_544.34585" defaultArrayLength="1353">
           <cvParam cvRef="MS" accession="MS:1001473" name="selected reaction monitoring chromatogram" value=""/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <userParam name="MS_dwell_time" value="0.10000000000000001" type="xs:float"/>
@@ -1307,7 +1307,7 @@
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
-              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="0.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
+              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="24.7712059021" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
             </activation>
           </precursor>
           <product>
@@ -1330,7 +1330,7 @@
             </binaryDataArray>
           </binaryDataArrayList>
         </chromatogram>
-        <chromatogram index="39" id="SRM SIC Q1=475.906 Q3=657.43 sample=1 period=1 experiment=1 transition=37" defaultArrayLength="1353">
+        <chromatogram index="39" id="SRM SIC Q1=475.906 Q3=657.43 sample=1 period=1 experiment=1 transition=37 ce=24.7712 name=H-PIN9_475.91_657.42991" defaultArrayLength="1353">
           <cvParam cvRef="MS" accession="MS:1001473" name="selected reaction monitoring chromatogram" value=""/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
           <userParam name="MS_dwell_time" value="0.10000000000000001" type="xs:float"/>
@@ -1340,7 +1340,7 @@
             </isolationWindow>
             <activation>
               <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
-              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="0.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
+              <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="24.7712059021" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
             </activation>
           </precursor>
           <product>
@@ -1370,48 +1370,48 @@
     <index name="spectrum">
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">3996</offset>
-      <offset idRef="BPC">19386</offset>
-      <offset idRef="SRM SIC Q1=264.114 Q3=396.129 sample=1 period=1 experiment=1 transition=0">34391</offset>
-      <offset idRef="SRM SIC Q1=264.114 Q3=395.204 sample=1 period=1 experiment=1 transition=1">48093</offset>
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-      <offset idRef="SRM SIC Q1=318.468 Q3=501.246 sample=1 period=1 experiment=1 transition=4">89061</offset>
-      <offset idRef="SRM SIC Q1=318.468 Q3=558.268 sample=1 period=1 experiment=1 transition=5">102061</offset>
-      <offset idRef="SRM SIC Q1=526.732 Q3=477.15 sample=1 period=1 experiment=1 transition=6">115581</offset>
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-      <offset idRef="SRM SIC Q1=351.491 Q3=772.315 sample=1 period=1 experiment=1 transition=8">142653</offset>
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-      <offset idRef="SRM SIC Q1=351.491 Q3=281.15 sample=1 period=1 experiment=1 transition=10">168653</offset>
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-      <offset idRef="SRM SIC Q1=405.845 Q3=281.15 sample=1 period=1 experiment=1 transition=14">220708</offset>
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-      <offset idRef="SRM SIC Q1=345.113 Q3=509.172 sample=1 period=1 experiment=1 transition=22">328456</offset>
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-      <offset idRef="SRM SIC Q1=529.234 Q3=651.246 sample=1 period=1 experiment=1 transition=29">422165</offset>
-      <offset idRef="SRM SIC Q1=529.234 Q3=832.276 sample=1 period=1 experiment=1 transition=30">435392</offset>
-      <offset idRef="SRM SIC Q1=529.234 Q3=945.36 sample=1 period=1 experiment=1 transition=31">448751</offset>
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-      <offset idRef="SRM SIC Q1=475.906 Q3=657.43 sample=1 period=1 experiment=1 transition=37">527959</offset>
+      <offset idRef="TIC">3997</offset>
+      <offset idRef="BPC">19399</offset>
+      <offset idRef="SRM SIC Q1=264.114 Q3=396.129 sample=1 period=1 experiment=1 transition=0 ce=13.9698 name=H-PIN1_264.11_396.12865">34416</offset>
+      <offset idRef="SRM SIC Q1=264.114 Q3=395.204 sample=1 period=1 experiment=1 transition=1 ce=13.9698 name=H-PIN1_264.11_395.20429">48170</offset>
+      <offset idRef="SRM SIC Q1=477.198 Q3=345.145 sample=1 period=1 experiment=1 transition=2 ce=26.4967 name=H-PIN2_477.2_345.14505">62360</offset>
+      <offset idRef="SRM SIC Q1=318.468 Q3=345.145 sample=1 period=1 experiment=1 transition=3 ce=16.7419 name=H-PIN2_318.47_345.14505">76009</offset>
+      <offset idRef="SRM SIC Q1=318.468 Q3=501.246 sample=1 period=1 experiment=1 transition=4 ce=16.7419 name=H-PIN2_318.47_501.24616">89293</offset>
+      <offset idRef="SRM SIC Q1=318.468 Q3=558.268 sample=1 period=1 experiment=1 transition=5 ce=16.7419 name=H-PIN2_318.47_558.26762">102345</offset>
+      <offset idRef="SRM SIC Q1=526.732 Q3=477.15 sample=1 period=1 experiment=1 transition=6 ce=28.6762 name=H-PIN3_526.73_477.15">115917</offset>
+      <offset idRef="SRM SIC Q1=351.491 Q3=396.129 sample=1 period=1 experiment=1 transition=7 ce=18.426 name=H-PIN3_351.49_396.12865">129525</offset>
+      <offset idRef="SRM SIC Q1=351.491 Q3=772.315 sample=1 period=1 experiment=1 transition=8 ce=18.426 name=H-PIN3_351.49_772.31455">143088</offset>
+      <offset idRef="SRM SIC Q1=526.732 Q3=657.336 sample=1 period=1 experiment=1 transition=9 ce=28.6762 name=H-PIN3_526.73_657.33603">156156</offset>
+      <offset idRef="SRM SIC Q1=351.491 Q3=281.15 sample=1 period=1 experiment=1 transition=10 ce=18.426 name=H-PIN3_351.49_281.15013">169190</offset>
+      <offset idRef="SRM SIC Q1=608.264 Q3=820.399 sample=1 period=1 experiment=1 transition=11 ce=32.2636 name=H-PIN4_608.26_820.39936">182827</offset>
+      <offset idRef="SRM SIC Q1=405.845 Q3=607.277 sample=1 period=1 experiment=1 transition=12 ce=21.1981 name=H-PIN4_405.85_607.27679">195745</offset>
+      <offset idRef="SRM SIC Q1=405.845 Q3=820.399 sample=1 period=1 experiment=1 transition=13 ce=21.1981 name=H-PIN4_405.85_820.39936">208612</offset>
+      <offset idRef="SRM SIC Q1=405.845 Q3=281.15 sample=1 period=1 experiment=1 transition=14 ce=21.1981 name=H-PIN4_405.85_281.15013">221451</offset>
+      <offset idRef="SRM SIC Q1=541.221 Q3=318.112 sample=1 period=1 experiment=1 transition=15 ce=29.3137 name=H-PIN5_541.22_318.112157">235298</offset>
+      <offset idRef="SRM SIC Q1=361.15 Q3=499.142 sample=1 period=1 experiment=1 transition=16 ce=18.9187 name=H-PIN5_361.15_499.141595">248546</offset>
+      <offset idRef="SRM SIC Q1=541.221 Q3=583.301 sample=1 period=1 experiment=1 transition=17 ce=29.3137 name=H-PIN5_541.22_583.301068">261557</offset>
+      <offset idRef="SRM SIC Q1=541.221 Q3=764.331 sample=1 period=1 experiment=1 transition=18 ce=29.3137 name=H-PIN5_541.22_764.330506">274877</offset>
+      <offset idRef="SRM SIC Q1=541.221 Q3=945.36 sample=1 period=1 experiment=1 transition=19 ce=29.3137 name=H-PIN5_541.22_945.359944">288349</offset>
+      <offset idRef="SRM SIC Q1=361.15 Q3=260.197 sample=1 period=1 experiment=1 transition=20 ce=18.9187 name=H-PIN5_361.15_260.19741">301860</offset>
+      <offset idRef="SRM SIC Q1=345.113 Q3=259.16 sample=1 period=1 experiment=1 transition=21 ce=20.685 name=H-PIN6_345.11_259.16">315811</offset>
+      <offset idRef="SRM SIC Q1=345.113 Q3=509.172 sample=1 period=1 experiment=1 transition=22 ce=20.685 name=H-PIN6_345.11_509.172226">329615</offset>
+      <offset idRef="SRM SIC Q1=487.187 Q3=541.254 sample=1 period=1 experiment=1 transition=23 ce=26.9362 name=H-PIN7_487.19_541.254118">343057</offset>
+      <offset idRef="SRM SIC Q1=487.187 Q3=722.284 sample=1 period=1 experiment=1 transition=24 ce=26.9362 name=H-PIN7_487.19_722.283556">356496</offset>
+      <offset idRef="SRM SIC Q1=487.187 Q3=903.313 sample=1 period=1 experiment=1 transition=25 ce=26.9362 name=H-PIN7_487.19_903.312994">369887</offset>
+      <offset idRef="SRM SIC Q1=487.187 Q3=360.225 sample=1 period=1 experiment=1 transition=26 ce=26.9362 name=H-PIN7_487.19_360.22468">383017</offset>
+      <offset idRef="SRM SIC Q1=529.234 Q3=185.1 sample=1 period=1 experiment=1 transition=27 ce=28.7863 name=H-PIN8_529.23_185.1">396732</offset>
+      <offset idRef="SRM SIC Q1=529.234 Q3=477.15 sample=1 period=1 experiment=1 transition=28 ce=28.7863 name=H-PIN8_529.23_477.15">410198</offset>
+      <offset idRef="SRM SIC Q1=529.234 Q3=651.246 sample=1 period=1 experiment=1 transition=29 ce=28.7863 name=H-PIN8_529.23_651.246446">423683</offset>
+      <offset idRef="SRM SIC Q1=529.234 Q3=832.276 sample=1 period=1 experiment=1 transition=30 ce=28.7863 name=H-PIN8_529.23_832.275884">436963</offset>
+      <offset idRef="SRM SIC Q1=529.234 Q3=945.36 sample=1 period=1 experiment=1 transition=31 ce=28.7863 name=H-PIN8_529.23_945.359944">450375</offset>
+      <offset idRef="SRM SIC Q1=529.234 Q3=470.217 sample=1 period=1 experiment=1 transition=32 ce=28.7863 name=H-PIN8_529.23_470.217008">463690</offset>
+      <offset idRef="SRM SIC Q1=713.355 Q3=838.459 sample=1 period=1 experiment=1 transition=33 ce=36.8876 name=H-PIN9_713.36_838.459348">477362</offset>
+      <offset idRef="SRM SIC Q1=713.355 Q3=1200.52 sample=1 period=1 experiment=1 transition=34 ce=36.8876 name=H-PIN9_713.36_1200.518224">490334</offset>
+      <offset idRef="SRM SIC Q1=713.355 Q3=657.43 sample=1 period=1 experiment=1 transition=35 ce=36.8876 name=H-PIN9_713.36_657.42991">503384</offset>
+      <offset idRef="SRM SIC Q1=475.906 Q3=544.346 sample=1 period=1 experiment=1 transition=36 ce=24.7712 name=H-PIN9_475.91_544.34585">516562</offset>
+      <offset idRef="SRM SIC Q1=475.906 Q3=657.43 sample=1 period=1 experiment=1 transition=37 ce=24.7712 name=H-PIN9_475.91_657.42991">529898</offset>
     </index>
   </indexList>
-  <indexListOffset>541313</indexListOffset>
-  <fileChecksum>0cd2cf3be0590dde1d78cb15a4e3d395534f90d5</fileChecksum>
+  <indexListOffset>543302</indexListOffset>
+  <fileChecksum>2c6c1e8dc8390cf321e26e07fe10320a9b6851b4</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/ThyroglobMRM000003.mzML b/tools/msconvert/test-data/ThyroglobMRM000003.mzML
index 1a9516f5d..5f44baecc 100644
--- a/tools/msconvert/test-data/ThyroglobMRM000003.mzML
+++ b/tools/msconvert/test-data/ThyroglobMRM000003.mzML
@@ -2,7 +2,7 @@
 <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="ThyroglobMRM000003" version="1.1.0">
     <cvList count="2">
-      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -24,18 +24,18 @@
     </fileDescription>
     <referenceableParamGroupList count="1">
       <referenceableParamGroup id="CommonInstrumentParams">
-        <cvParam cvRef="MS" accession="MS:1000122" name="Bruker Daltonics instrument model" value=""/>
+        <cvParam cvRef="MS" accession="MS:1003123" name="Bruker Daltonics timsTOF series" value=""/>
       </referenceableParamGroup>
     </referenceableParamGroupList>
     <softwareList count="3">
-      <software id="TIMS_SDK" version="2.3.101.131-791">
+      <software id="TIMS_SDK" version="2.21.104.32">
         <cvParam cvRef="MS" accession="MS:1000692" name="Bruker software" value=""/>
         <userParam name="software name" value="TIMS SDK"/>
       </software>
       <software id="micrOTOFcontrol" version="5.0.71.422-9346-vc110">
         <cvParam cvRef="MS" accession="MS:1000726" name="micrOTOFcontrol" value=""/>
       </software>
-      <software id="pwiz_Reader_Bruker" version="3.0.20287">
+      <software id="pwiz_Reader_Bruker" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -69,6 +69,13 @@
         <processingMethod order="0" softwareRef="pwiz_Reader_Bruker">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
+        <processingMethod order="1" softwareRef="pwiz_Reader_Bruker">
+          <userParam name="summing of spectra from the same precursor adjacent in time and/or mobility space"/>
+          <userParam name="m/z tolerance" value="0.05" type="xsd:double"/>
+          <userParam name="scan time tolerance" value="10.0" type="xsd:double"/>
+          <userParam name="ion mobility tolerance" value="0.01" type="xsd:double"/>
+          <userParam name="sumMS1" value="false" type="xsd:boolean"/>
+        </processingMethod>
       </dataProcessing>
     </dataProcessingList>
     <run id="ThyroglobMRM000003" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2017-06-23T18:24:10Z" defaultSourceFileRef="ThyroglobMRM000003.d_x005c_Analysis.tdf">
@@ -180,13 +187,13 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
-      <offset idRef="merged=0 frame=1 scanStart=1 scanEnd=2742">4696</offset>
+      <offset idRef="merged=0 frame=1 scanStart=1 scanEnd=2742">5211</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">395653</offset>
-      <offset idRef="BPC">397388</offset>
+      <offset idRef="TIC">396168</offset>
+      <offset idRef="BPC">397903</offset>
     </index>
   </indexList>
-  <indexListOffset>399155</indexListOffset>
-  <fileChecksum>7047bda27420524fb4c405ab749301343ae7d839</fileChecksum>
+  <indexListOffset>399670</indexListOffset>
+  <fileChecksum>555748f5c21d7e5d15882040d42f6f287e2e5e48</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-activation.mzML b/tools/msconvert/test-data/small-activation.mzML
index 2de5bef54..823af79d5 100644
--- a/tools/msconvert/test-data/small-activation.mzML
+++ b/tools/msconvert/test-data/small-activation.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;activation CID&quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2717,59 +2719,59 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">482266</offset>
+      <offset idRef="TIC">482641</offset>
     </index>
   </indexList>
-  <indexListOffset>484216</indexListOffset>
-  <fileChecksum>8b12e89899d385d5ef0b007114bc36001c18198e</fileChecksum>
+  <indexListOffset>484591</indexListOffset>
+  <fileChecksum>f227f70cb3fe96b9c843367e44bf189fc882628d</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-analyzer-filter.mzML b/tools/msconvert/test-data/small-analyzer-filter.mzML
index cee2aa500..543de02cf 100644
--- a/tools/msconvert/test-data/small-analyzer-filter.mzML
+++ b/tools/msconvert/test-data/small-analyzer-filter.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;analyzer IT&quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2437,52 +2439,52 @@
   </mzML>
   <indexList count="2">
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     <index name="chromatogram">
-      <offset idRef="TIC">420845</offset>
+      <offset idRef="TIC">421217</offset>
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   </indexList>
-  <indexListOffset>422795</indexListOffset>
-  <fileChecksum>e9998c0aa79067dc7935ea57633613380f9eef85</fileChecksum>
+  <indexListOffset>423167</indexListOffset>
+  <fileChecksum>f01f48f7098df6559262c90d561b382a6f490668</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-chargeStatePredictor.mzML b/tools/msconvert/test-data/small-chargeStatePredictor.mzML
index 4a4bc1418..8122f419c 100644
--- a/tools/msconvert/test-data/small-chargeStatePredictor.mzML
+++ b/tools/msconvert/test-data/small-chargeStatePredictor.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;chargeStatePredictor overrideExistingCharge=true minMultipleCharge=2 maxMultipleCharge=5 singleChargeFractionTIC=0.95 maxKnownCharge=8&quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2847,59 +2849,59 @@
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   <indexList count="2">
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     <index name="chromatogram">
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-  <fileChecksum>820300fdfbf32732fca84c471e7509c5cfee54de</fileChecksum>
+  <indexListOffset>497953</indexListOffset>
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 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-deisotope.mzML b/tools/msconvert/test-data/small-deisotope.mzML
index 55ad34588..f2fd7a98f 100644
--- a/tools/msconvert/test-data/small-deisotope.mzML
+++ b/tools/msconvert/test-data/small-deisotope.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -20,7 +20,7 @@
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         </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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
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       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
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         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter MS2Deisotope --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2717,59 +2719,59 @@
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">414467</offset>
+      <offset idRef="TIC">414828</offset>
     </index>
   </indexList>
-  <indexListOffset>416417</indexListOffset>
-  <fileChecksum>4905286e336a1eefdef42b1db55dbfb78533d42f</fileChecksum>
+  <indexListOffset>416778</indexListOffset>
+  <fileChecksum>a59fe78d9d9997ca1a37cc1e3b2e4a3b77eaa937</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-denoise.mzML b/tools/msconvert/test-data/small-denoise.mzML
index 777320b1c..d165d3240 100644
--- a/tools/msconvert/test-data/small-denoise.mzML
+++ b/tools/msconvert/test-data/small-denoise.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;MS2Denoise 10 40.0 false&quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2717,59 +2719,59 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">368659</offset>
+      <offset idRef="TIC">369044</offset>
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   </indexList>
-  <indexListOffset>370609</indexListOffset>
-  <fileChecksum>3bb136dddbbf1dbe75414cfeb9b330cbc887d232</fileChecksum>
+  <indexListOffset>370994</indexListOffset>
+  <fileChecksum>aa7b321dcb13501ce6eb76c4d3169ec55125fcad</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-index-filter.mzML b/tools/msconvert/test-data/small-index-filter.mzML
index b2abe084d..5aeeccaa6 100644
--- a/tools/msconvert/test-data/small-index-filter.mzML
+++ b/tools/msconvert/test-data/small-index-filter.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;scanNumber [3,5] [11,11] [14,16] &quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -497,18 +499,18 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">76431</offset>
+      <offset idRef="TIC">76825</offset>
     </index>
   </indexList>
-  <indexListOffset>78381</indexListOffset>
-  <fileChecksum>190e7438359420dfb1a9b11d5829700a34ec36bd</fileChecksum>
+  <indexListOffset>78775</indexListOffset>
+  <fileChecksum>ecc985036748acf557789e39e46f4175163c16e1</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-ms-level-filter.mzML b/tools/msconvert/test-data/small-ms-level-filter.mzML
index 48b337923..53f98dd35 100644
--- a/tools/msconvert/test-data/small-ms-level-filter.mzML
+++ b/tools/msconvert/test-data/small-ms-level-filter.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;msLevel [2, 2]&quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2157,45 +2159,45 @@
   </mzML>
   <indexList count="2">
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     <index name="chromatogram">
-      <offset idRef="TIC">347749</offset>
+      <offset idRef="TIC">348124</offset>
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   </indexList>
-  <indexListOffset>349699</indexListOffset>
-  <fileChecksum>4fc5cbcd6dd3aef49694e162339328aa1da1ac72</fileChecksum>
+  <indexListOffset>350074</indexListOffset>
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 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-mzWindow.mzML b/tools/msconvert/test-data/small-mzWindow.mzML
index b25123f79..022a6e610 100644
--- a/tools/msconvert/test-data/small-mzWindow.mzML
+++ b/tools/msconvert/test-data/small-mzWindow.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;mzWindow [420.0,840.0]&quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -128,7 +130,7 @@
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-              <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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-              <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value=""/>
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">330052</offset>
+      <offset idRef="TIC">334227</offset>
     </index>
   </indexList>
-  <indexListOffset>332002</indexListOffset>
-  <fileChecksum>c854b1b0a8acbad401bff243741e2b6e87b59921</fileChecksum>
+  <indexListOffset>336177</indexListOffset>
+  <fileChecksum>4702759a587f3263321a392921338173de2f58a3</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-numpressL.mzML b/tools/msconvert/test-data/small-numpressL.mzML
index f0a54bb9e..20fa55cd5 100644
--- a/tools/msconvert/test-data/small-numpressL.mzML
+++ b/tools/msconvert/test-data/small-numpressL.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --mz64 --inten32 --numpressLinear --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2717,59 +2719,59 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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     <index name="chromatogram">
-      <offset idRef="TIC">596579</offset>
+      <offset idRef="TIC">596904</offset>
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   </indexList>
-  <indexListOffset>598553</indexListOffset>
-  <fileChecksum>9e8a7e09b1378d24473ee14679c2702bbe4d7dcd</fileChecksum>
+  <indexListOffset>598878</indexListOffset>
+  <fileChecksum>413bb54f4eb0bf27611e573f22d1d5324051c120</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-numpressLP.mzML b/tools/msconvert/test-data/small-numpressLP.mzML
index 2de5bef54..b71fd0285 100644
--- a/tools/msconvert/test-data/small-numpressLP.mzML
+++ b/tools/msconvert/test-data/small-numpressLP.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2717,59 +2719,59 @@
   </mzML>
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">482266</offset>
+      <offset idRef="TIC">482605</offset>
     </index>
   </indexList>
-  <indexListOffset>484216</indexListOffset>
-  <fileChecksum>8b12e89899d385d5ef0b007114bc36001c18198e</fileChecksum>
+  <indexListOffset>484555</indexListOffset>
+  <fileChecksum>66dc8793741a6d2e90608d228775bdd9fe062024</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-numpressLS.mzML b/tools/msconvert/test-data/small-numpressLS.mzML
index 01b2b7d73..d61f07413 100644
--- a/tools/msconvert/test-data/small-numpressLS.mzML
+++ b/tools/msconvert/test-data/small-numpressLS.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --mz64 --inten32 --numpressLinear --numpressSlof --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2717,59 +2719,59 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">500531</offset>
+      <offset idRef="TIC">500871</offset>
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   </indexList>
-  <indexListOffset>502417</indexListOffset>
-  <fileChecksum>d2b87f8909ac1ac2841f31da0f78c308b3df311f</fileChecksum>
+  <indexListOffset>502757</indexListOffset>
+  <fileChecksum>d97cffe36ac0a16e2f7715f82ecc39dba5f02152</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-numpressP.mzML b/tools/msconvert/test-data/small-numpressP.mzML
index da3af77d2..2b242c367 100644
--- a/tools/msconvert/test-data/small-numpressP.mzML
+++ b/tools/msconvert/test-data/small-numpressP.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --mz64 --inten32 --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2717,59 +2719,59 @@
   </mzML>
   <indexList count="2">
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=48">688732</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">701461</offset>
+      <offset idRef="TIC">701783</offset>
     </index>
   </indexList>
-  <indexListOffset>703411</indexListOffset>
-  <fileChecksum>9c5dabb4b727d6bd3171e261e16eda5a4a9a5f83</fileChecksum>
+  <indexListOffset>703733</indexListOffset>
+  <fileChecksum>d9c1fa40c417046e32fa0f5e2b3e2802159f7669</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-numpressS.mzML b/tools/msconvert/test-data/small-numpressS.mzML
index f3f90b6cd..5451fb9cc 100644
--- a/tools/msconvert/test-data/small-numpressS.mzML
+++ b/tools/msconvert/test-data/small-numpressS.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --mz64 --inten32 --numpressSlof --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2717,59 +2719,59 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">719726</offset>
+      <offset idRef="TIC">720049</offset>
     </index>
   </indexList>
-  <indexListOffset>721612</indexListOffset>
-  <fileChecksum>e0fd56c8c54f59e8f6b811b22b81422e56803d8c</fileChecksum>
+  <indexListOffset>721935</indexListOffset>
+  <fileChecksum>c755f2904824995e95b6f4eee3125ee7c2359626</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-peakpicking-cwt-MS1.mzML b/tools/msconvert/test-data/small-peakpicking-cwt-MS1.mzML
new file mode 100644
index 000000000..43a7152d4
--- /dev/null
+++ b/tools/msconvert/test-data/small-peakpicking-cwt-MS1.mzML
@@ -0,0 +1,2774 @@
+<?xml version="1.0" encoding="utf-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="4.1.117" 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>
+        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
+        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
+      </fileContent>
+      <sourceFileList count="2">
+        <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"/>
+        </sourceFile>
+        <sourceFile id="small.mzML" name="small.mzML" location="file:///">
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>
+        </sourceFile>
+      </sourceFileList>
+    </fileDescription>
+    <referenceableParamGroupList count="1">
+      <referenceableParamGroup id="CommonInstrumentParams">
+        <cvParam cvRef="MS" accession="MS:1000448" name="LTQ FT" value=""/>
+        <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>
+      </referenceableParamGroup>
+    </referenceableParamGroupList>
+    <softwareList count="3">
+      <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_3.0.23187" version="3.0.23187">
+        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
+      </software>
+    </softwareList>
+    <instrumentConfigurationList count="2">
+      <instrumentConfiguration id="IC1">
+        <referenceableParamGroupRef ref="CommonInstrumentParams"/>
+        <componentList count="3">
+          <source order="1">
+            <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
+            <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/>
+          </source>
+          <analyzer order="2">
+            <cvParam cvRef="MS" accession="MS:1000079" name="fourier transform ion cyclotron resonance mass spectrometer" value=""/>
+          </analyzer>
+          <detector order="3">
+            <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>
+          </detector>
+        </componentList>
+        <softwareRef ref="Xcalibur"/>
+      </instrumentConfiguration>
+      <instrumentConfiguration id="IC2">
+        <referenceableParamGroupRef ref="CommonInstrumentParams"/>
+        <componentList count="3">
+          <source order="1">
+            <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
+            <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/>
+          </source>
+          <analyzer order="2">
+            <cvParam cvRef="MS" accession="MS:1000083" name="radial ejection linear ion trap" value=""/>
+          </analyzer>
+          <detector order="3">
+            <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>
+          </detector>
+        </componentList>
+        <softwareRef ref="Xcalibur"/>
+      </instrumentConfiguration>
+    </instrumentConfigurationList>
+    <dataProcessingList count="2">
+      <dataProcessing id="pwiz_Reader_Thermo_conversion">
+        <processingMethod order="0" softwareRef="pwiz">
+          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;peakPicking cwt msLevel=1&quot; --mz64 --inten32 --zlib --outfile small"/>
+        </processingMethod>
+      </dataProcessing>
+      <dataProcessing id="pwiz_Reader_conversion">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
+          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+        </processingMethod>
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
+          <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
+          <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
+        </processingMethod>
+      </dataProcessing>
+    </dataProcessingList>
+    <run id="small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2005-07-20T14:44:22Z" defaultSourceFileRef="RAW1">
+      <spectrumList count="48" defaultDataProcessingRef="pwiz_Reader_conversion">
+        <spectrum index="0" id="controllerType=0 controllerNumber=1 scan=1" defaultArrayLength="723" dataProcessingRef="pwiz_Reader_conversion">
+          <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
+          <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="810.415283203125" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+          <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="1.471973875e06" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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+          <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
+          <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
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+          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1.14331703125e05"/>
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+            <scan instrumentConfigurationRef="IC2">
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+              <userParam name="[Thermo Trailer Extra]Monoisotopic M/Z:" value="0" type="xsd:float"/>
+              <scanWindowList count="1">
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+          <precursorList count="1">
+            <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=2">
+              <isolationWindow>
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+                <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="1.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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+              </isolationWindow>
+              <selectedIonList count="1">
+                <selectedIon>
+                  <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="725.36" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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+                </selectedIon>
+              </selectedIonList>
+              <activation>
+                <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
+                <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="35.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
+              </activation>
+            </precursor>
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+          <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
+          <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
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+          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1.7613074e07"/>
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+          <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="2000.009946620377" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+          <scanList count="1">
+            <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
+            <scan>
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+              <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="FTMS + p ESI Full ms [200.00-2000.00]"/>
+              <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="1"/>
+              <cvParam cvRef="MS" accession="MS:1000927" name="ion injection time" value="78.409637451172" unitCvRef="UO" unitAccession="UO:0000028" unitName="millisecond"/>
+              <scanWindowList count="1">
+                <scanWindow>
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+                </scanWindow>
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+            </scan>
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+              <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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+          <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
+          <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="810.636352539063" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+          <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="1.744729375e05" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
+          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1.3332331e07"/>
+          <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="200.090909093618" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+          <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="2000.00005364418" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+          <scanList count="1">
+            <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
+            <scan instrumentConfigurationRef="IC2">
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+              <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS + p ESI Full ms [200.00-2000.00]"/>
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+              <cvParam cvRef="MS" accession="MS:1000927" name="ion injection time" value="2.420493364334" unitCvRef="UO" unitAccession="UO:0000028" unitName="millisecond"/>
+              <scanWindowList count="1">
+                <scanWindow>
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+              <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
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+          <cvParam cvRef="MS" accession="MS:1000235" name="total ion current chromatogram" value=""/>
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diff --git a/tools/msconvert/test-data/small-peakpicking-cwt-allMS.mzML b/tools/msconvert/test-data/small-peakpicking-cwt-allMS.mzML
index 79cb91b33..43a7152d4 100644
--- a/tools/msconvert/test-data/small-peakpicking-cwt-allMS.mzML
+++ b/tools/msconvert/test-data/small-peakpicking-cwt-allMS.mzML
@@ -2,7 +2,7 @@
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   <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">
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+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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"/>
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       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
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     </softwareList>
@@ -76,15 +76,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
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         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
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+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
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         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
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           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=32">396701</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=33">408129</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=34">420030</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=35">430856</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=39">479578</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=41">504470</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=43">540156</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=44">555316</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=45">566370</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=46">581111</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=47">593095</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=48">604617</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">615694</offset>
+      <offset idRef="TIC">616012</offset>
     </index>
   </indexList>
-  <indexListOffset>617704</indexListOffset>
-  <fileChecksum>2ae454603847b07c7951a779a4c92eacefa07d13</fileChecksum>
+  <indexListOffset>618022</indexListOffset>
+  <fileChecksum>2521de75b7feb9f92ba940bd71b7ea87c3149c84</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-peakpicking-vendor-allMS.mzML b/tools/msconvert/test-data/small-peakpicking-vendor-allMS.mzML
index 55b88ee81..d4c2615e5 100644
--- a/tools/msconvert/test-data/small-peakpicking-vendor-allMS.mzML
+++ b/tools/msconvert/test-data/small-peakpicking-vendor-allMS.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -33,7 +33,7 @@
       <software id="Xcalibur" version="1.1 Beta 7">
         <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
       </software>
-      <software id="pwiz" version="3.0.20287">
+      <software id="pwiz" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -2748,59 +2748,59 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
-      <offset idRef="controllerType=0 controllerNumber=1 scan=1">4871</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=1">4872</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=48">730430</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">741908</offset>
+      <offset idRef="TIC">741909</offset>
     </index>
   </indexList>
-  <indexListOffset>744444</indexListOffset>
-  <fileChecksum>3c66afcb2b2b84417b41294c8b47550ca7803765</fileChecksum>
+  <indexListOffset>744445</indexListOffset>
+  <fileChecksum>9cff4bb31276cc7701ea1f33e62f003752957b6b</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-polarity-filter.mzML b/tools/msconvert/test-data/small-polarity-filter.mzML
index 2de5bef54..a8a83b0e4 100644
--- a/tools/msconvert/test-data/small-polarity-filter.mzML
+++ b/tools/msconvert/test-data/small-polarity-filter.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;polarity positive&quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2717,59 +2719,59 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">482266</offset>
+      <offset idRef="TIC">482644</offset>
     </index>
   </indexList>
-  <indexListOffset>484216</indexListOffset>
-  <fileChecksum>8b12e89899d385d5ef0b007114bc36001c18198e</fileChecksum>
+  <indexListOffset>484594</indexListOffset>
+  <fileChecksum>b9a59011277763f03b0f9425e8f00885fd3d8839</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-strip-it.mzML b/tools/msconvert/test-data/small-strip-it.mzML
index 939b1a059..512a00f57 100644
--- a/tools/msconvert/test-data/small-strip-it.mzML
+++ b/tools/msconvert/test-data/small-strip-it.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter stripIT --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2437,52 +2439,52 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">409170</offset>
+      <offset idRef="TIC">409526</offset>
     </index>
   </indexList>
-  <indexListOffset>411120</indexListOffset>
-  <fileChecksum>e01428f6ebeb6b29c2d2bf8548e2ee684824a0e0</fileChecksum>
+  <indexListOffset>411476</indexListOffset>
+  <fileChecksum>2411a6b7a7c1d459f9ef4999cb163dd37acd5650</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-threshold.mzML b/tools/msconvert/test-data/small-threshold.mzML
index eba07f0f1..1297229fa 100644
--- a/tools/msconvert/test-data/small-threshold.mzML
+++ b/tools/msconvert/test-data/small-threshold.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;threshold count 100.0 most-intense&quot; --filter &quot;threshold absolute 1.0 most-intense&quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2717,59 +2719,59 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">270993</offset>
+      <offset idRef="TIC">271445</offset>
     </index>
   </indexList>
-  <indexListOffset>272943</indexListOffset>
-  <fileChecksum>95a42b81dbc77e94be64a5f6577fe211616e6069</fileChecksum>
+  <indexListOffset>273395</indexListOffset>
+  <fileChecksum>bdb74b38772dab34977d072c388a89251b5dce20</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-turbocharger.mzML b/tools/msconvert/test-data/small-turbocharger.mzML
index 59acbb031..3baa90309 100644
--- a/tools/msconvert/test-data/small-turbocharger.mzML
+++ b/tools/msconvert/test-data/small-turbocharger.mzML
@@ -2,7 +2,7 @@
 <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="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" 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>
@@ -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="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7e353c5db740e14ea07773d36483f22627aef770"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.20287" version="3.0.20287">
+      <software id="pwiz_3.0.23187" version="3.0.23187">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,15 +79,17 @@
       <dataProcessing id="pwiz_Reader_Thermo_conversion">
         <processingMethod order="0" softwareRef="pwiz">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+          <cvParam cvRef="MS" accession="MS:1001885" name="command-line parameters" value="small-peakpicking-cwt-allMS.mzML --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter &quot;turbocharger minCharge=1 maxCharge=5 precursorsBefore=1 precursorsAfter=1 halfIsoWidth=1.5 defaultMinCharge=1 defaultMaxCharge=5&quot; --mz64 --inten32 --numpressLinear --numpressPic --outfile small-peakpicking-cwt-allMS"/>
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="0" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
+        <processingMethod order="1" softwareRef="pwiz_3.0.23187">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
           <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
+          <userParam name="ms levels" value="[1,1]"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2754,59 +2756,59 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
-      <offset idRef="controllerType=0 controllerNumber=1 scan=1">5614</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=1">6103</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=19">185337</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=21">204436</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=22">215340</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=23">223255</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=24">231911</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=25">241174</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=26">252704</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=27">262899</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=28">272515</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=30">291624</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=31">301986</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=32">313472</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=33">322890</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=34">332600</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=35">341513</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=36">349084</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=37">358101</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=38">367319</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=39">379650</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=42">409911</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=44">434793</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=45">444223</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=46">456129</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=47">465954</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=48">475406</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">484192</offset>
+      <offset idRef="TIC">484681</offset>
     </index>
   </indexList>
-  <indexListOffset>486142</indexListOffset>
-  <fileChecksum>cd24511f35d08aae98099af6b561206194199d9a</fileChecksum>
+  <indexListOffset>486631</indexListOffset>
+  <fileChecksum>d3b18f08fb5781b84815d1ee21b69203756f538f</fileChecksum>
 </indexedmzML>
diff --git a/tools/msconvert/test-data/small-zlib-32.mzXML b/tools/msconvert/test-data/small-zlib-32.mzXML
index 5c8821985..dd1497d73 100644
--- a/tools/msconvert/test-data/small-zlib-32.mzXML
+++ b/tools/msconvert/test-data/small-zlib-32.mzXML
@@ -27,13 +27,14 @@
       <processingOperation name="Conversion to mzML"/>
     </dataProcessing>
     <dataProcessing>
-      <software type="conversion" name="ProteoWizard software" version="3.0.20287"/>
+      <software type="conversion" name="ProteoWizard software" version="3.0.23187"/>
       <processingOperation name="Conversion to mzML"/>
     </dataProcessing>
     <dataProcessing centroided="1">
-      <software type="processing" name="ProteoWizard software" version="3.0.20287"/>
+      <software type="processing" name="ProteoWizard software" version="3.0.23187"/>
       <processingOperation name="peak picking"/>
       <comment>CantWaiT (continuous wavelet transform) peak picker</comment>
+      <comment>ms levels: [1,1]</comment>
     </dataProcessing>
     <scan num="1"
           scanType="Full"
@@ -1017,55 +1018,55 @@
     </scan>
   </msRun>
   <index name="scan">
-    <offset id="1">2216</offset>
-    <offset id="2">9801</offset>
-    <offset id="3">19280</offset>
-    <offset id="4">24800</offset>
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-    <offset id="6">44377</offset>
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-    <offset id="45">357206</offset>
-    <offset id="46">367817</offset>
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-    <offset id="48">382881</offset>
+    <offset id="1">2258</offset>
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+    <offset id="3">19322</offset>
+    <offset id="4">24842</offset>
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+    <offset id="6">44419</offset>
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+    <offset id="29">225376</offset>
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+    <offset id="31">240747</offset>
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+    <offset id="43">340496</offset>
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+    <offset id="45">357248</offset>
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+    <offset id="47">375632</offset>
+    <offset id="48">382923</offset>
   </index>
-  <indexOffset>389941</indexOffset>
-  <sha1>031f5f799e75da3c5f997d718cfdd7ccdc1b5672</sha1>
+  <indexOffset>389983</indexOffset>
+  <sha1>9520f0742f1bad55e5b1e8c51603f84a853f86d3</sha1>
 </mzXML>
diff --git a/tools/msconvert/test-data/small-zlib-64.mz5 b/tools/msconvert/test-data/small-zlib-64.mz5
index 453976294..840b1acc8 100644
Binary files a/tools/msconvert/test-data/small-zlib-64.mz5 and b/tools/msconvert/test-data/small-zlib-64.mz5 differ