Merge branch 'ProteoWizard:master' into master

ProteoWizard · Aug 26, 2022 · 9fd77a6 · 9fd77a6
2 parents 3daf440 + a2889c1
commit 9fd77a6
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diff --git a/.github/workflows/cherrypick-pr-to-release.yml b/.github/workflows/cherrypick-pr-to-release.yml
@@ -16,6 +16,6 @@ jobs:
     - name: Cherry pick PR to release
       uses: chambm/gh-backport-action@master
       with:
-        pr_branch: 'Skyline/skyline_21_2'
+        pr_branch: 'Skyline/skyline_22_2'
         pr_title: 'Automatic cherry pick of #{pr_number} from {base_branch} to {pr_branch}'
         github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/rebase_on_demand.yml b/.github/workflows/rebase_on_demand.yml
@@ -14,6 +14,6 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
           fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
       - name: Automatic Rebase
-        uses: cirrus-actions/rebase@1.4
+        uses: cirrus-actions/rebase@1.7
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/squash_on_demand.yml b/.github/workflows/squash_on_demand.yml
@@ -9,6 +9,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - uses: dekvall/softfix@v1.1
+    - uses: chambm/softfix@v2
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -390,6 +390,8 @@ Reader*Test.data
 /pwiz_aux/msrc/utility/vendor_api/ABI/LicenseKey.h
 /pwiz_aux/msrc/utility/vendor_api/Agilent/x64/
 /pwiz_aux/msrc/utility/vendor_api/Agilent/x86/
+/pwiz_aux/msrc/utility/vendor_api/Bruker/BAF2SQL-README.txt
+/pwiz_aux/msrc/utility/vendor_api/Bruker/BAF2SQL-THIRD-PARTY-LICENSE-README.txt
 /pwiz_aux/msrc/utility/vendor_api/Bruker/x64/
 /pwiz_aux/msrc/utility/vendor_api/Bruker/x86/
 /pwiz_aux/msrc/utility/vendor_api/Bruker/**/*.h

diff --git a/pwiz.vcxproj b/pwiz.vcxproj
@@ -18,7 +18,7 @@
     <ProjectGuid>{69BD51D3-2BBA-4462-A5A4-FC8EF88A52FD}</ProjectGuid>
     <RootNamespace>pwiz</RootNamespace>
     <Keyword>MakeFileProj</Keyword>
-    <WindowsTargetPlatformVersion>10.0.17134.0</WindowsTargetPlatformVersion>
+    <WindowsTargetPlatformVersion>10.0</WindowsTargetPlatformVersion>
     <TargetFrameworkVersion>4.7.2</TargetFrameworkVersion>
   </PropertyGroup>
   <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
@@ -30,7 +30,7 @@
     <CLRSupport>true</CLRSupport>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|x64'" Label="Configuration">
-    <PlatformToolset>v141</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <ConfigurationType>Application</ConfigurationType>
     <CharacterSet>MultiByte</CharacterSet>
     <CLRSupport>true</CLRSupport>
@@ -88,9 +88,17 @@
   </ItemDefinitionGroup>
   <ItemGroup>
     <ClCompile Include="libraries\boost_aux\libs\nowide\src\iostream.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramListFactory.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramListFactoryTest.cpp" />
     <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramListWrapperTest.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramList_Filter.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramList_FilterTest.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramList_LockmassRefiner.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramList_LockmassRefinerTest.cpp" />
     <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramList_SavitzkyGolaySmoother.cpp" />
     <ClCompile Include="pwiz\analysis\chromatogram_processing\SavitzkyGolaySmootherTest.cpp" />
+    <ClCompile Include="pwiz\analysis\common\CwtPeakDetector.cpp" />
+    <ClCompile Include="pwiz\analysis\common\CwtPeakDetectorTest.cpp" />
     <ClCompile Include="pwiz\analysis\common\ExtraZeroSamplesFilter.cpp" />
     <ClCompile Include="pwiz\analysis\common\ExtraZeroSamplesFilterTest.cpp" />
     <ClCompile Include="pwiz\analysis\common\LocalMaximumPeakDetector.cpp" />
@@ -327,6 +335,12 @@
     <ClCompile Include="pwiz\data\msdata\MSDataTest.cpp" />
     <ClCompile Include="pwiz\data\msdata\MSnReaderTest.cpp" />
     <ClCompile Include="pwiz\data\msdata\MSNumpress.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\Configuration_mz5.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\Connection_mz5.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\Datastructures_mz5.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\ReferenceRead_mz5.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\ReferenceWrite_mz5.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\Translator_mz5.cpp" />
     <ClCompile Include="pwiz\data\msdata\RAMPAdapter.cpp" />
     <ClCompile Include="pwiz\data\msdata\RAMPAdapterTest.cpp" />
     <ClCompile Include="pwiz\data\msdata\Reader.cpp" />
@@ -348,6 +362,7 @@
     <ClCompile Include="pwiz\data\msdata\SpectrumInfoTest.cpp" />
     <ClCompile Include="pwiz\data\msdata\SpectrumIterator.cpp" />
     <ClCompile Include="pwiz\data\msdata\SpectrumIteratorTest.cpp" />
+    <ClCompile Include="pwiz\data\msdata\SpectrumListBase.cpp" />
     <ClCompile Include="pwiz\data\msdata\SpectrumListBaseTest.cpp" />
     <ClCompile Include="pwiz\data\msdata\SpectrumListCache.cpp" />
     <ClCompile Include="pwiz\data\msdata\SpectrumListCacheTest.cpp" />
@@ -440,9 +455,11 @@
     <ClCompile Include="pwiz\data\vendor_readers\Thermo\Reader_Thermo_Detail.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\Thermo\Reader_Thermo_Test.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\Thermo\SpectrumList_Thermo.cpp" />
+    <ClCompile Include="pwiz\data\vendor_readers\UIMF\ChromatogramList_UIMF.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\UIMF\Reader_UIMF.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\UIMF\Reader_UIMF_Test.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\UIMF\SpectrumList_UIMF.cpp" />
+    <ClCompile Include="pwiz\data\vendor_readers\UNIFI\ChromatogramList_UNIFI.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\UNIFI\Reader_UNIFI_Test.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\UNIFI\Reader_UNIFI.cpp" />
     <ClCompile Include="pwiz\data\vendor_readers\UNIFI\Reader_UNIFI_Detail.cpp" />
@@ -465,6 +482,7 @@
       <PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|Win32'">PWIZ_READER_THERMO;PWIZ_READER_AGILENT;PWIZ_READER_BRUKER;PWIZ_READER_WATERS;PWIZ_READER_ABI;PWIZ_READER_ABI_T2D;WIN32;USE_RAW_PTR;PWIZ_BINDINGS_CLI_COMBINED;%(PreprocessorDefinitions)</PreprocessorDefinitions>
       <PreprocessorDefinitions Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|x64'">PWIZ_READER_THERMO;PWIZ_READER_AGILENT;PWIZ_READER_BRUKER;PWIZ_READER_WATERS;PWIZ_READER_ABI;PWIZ_READER_ABI_T2D;WIN32;USE_RAW_PTR;PWIZ_BINDINGS_CLI_COMBINED;%(PreprocessorDefinitions)</PreprocessorDefinitions>
     </ClCompile>
+    <ClCompile Include="pwiz\utility\bindings\CLI\analysis\SpectrumList_IonMobility_Test.cpp" />
     <ClCompile Include="pwiz\utility\bindings\CLI\analysis\SpectrumList_PeakFilter.cpp">
       <CompileAsManaged Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|Win32'">true</CompileAsManaged>
       <CompileAsManaged Condition="'$(Configuration)|$(Platform)'=='BrowseOnly|x64'">true</CompileAsManaged>
@@ -775,6 +793,7 @@
     <ClCompile Include="pwiz\utility\misc\SHA1Calculator.cpp" />
     <ClCompile Include="pwiz\utility\misc\SHA1CalculatorTest.cpp" />
     <ClCompile Include="pwiz\utility\misc\SHA1_ostream_test.cpp" />
+    <ClCompile Include="pwiz\utility\misc\String.cpp" />
     <ClCompile Include="pwiz\utility\misc\TabReader.cpp" />
     <ClCompile Include="pwiz\utility\misc\TabReaderTest.cpp" />
     <ClCompile Include="pwiz\utility\misc\VendorReaderTestHarness.cpp" />
@@ -849,6 +868,7 @@
     <ClCompile Include="pwiz_tools\BiblioSpec\tests\CompareTextFiles.cpp" />
     <ClCompile Include="pwiz_tools\BiblioSpec\tests\ExecuteBlib.cpp" />
     <ClCompile Include="pwiz_tools\commandline\chainsaw.cpp" />
+    <ClCompile Include="pwiz_tools\commandline\idcat.cpp" />
     <ClCompile Include="pwiz_tools\commandline\idconvert.cpp" />
     <ClCompile Include="pwiz_tools\commandline\msaccess.cpp" />
     <ClCompile Include="pwiz_tools\commandline\msconvert.cpp" />
@@ -886,6 +906,10 @@
     <ClInclude Include="libraries\boost_aux\boost\nowide\stackstring.hpp" />
     <ClInclude Include="libraries\boost_aux\boost\nowide\system.hpp" />
     <ClInclude Include="libraries\boost_aux\boost\nowide\windows.hpp" />
+    <ClInclude Include="pwiz\analysis\chromatogram_processing\ChromatogramListFactory.hpp" />
+    <ClInclude Include="pwiz\analysis\chromatogram_processing\ChromatogramList_Filter.hpp" />
+    <ClInclude Include="pwiz\analysis\chromatogram_processing\ChromatogramList_LockmassRefiner.hpp" />
+    <ClInclude Include="pwiz\analysis\common\CwtPeakDetector.hpp" />
     <ClInclude Include="pwiz\analysis\demux\CubicHermiteSpline.hpp" />
     <ClInclude Include="pwiz\analysis\demux\DemuxDataProcessingStrings.hpp" />
     <ClInclude Include="pwiz\analysis\demux\DemuxDebugReader.hpp" />
@@ -914,8 +938,10 @@
     <ClInclude Include="pwiz\analysis\proteome_processing\ProteinListFactory.hpp" />
     <ClInclude Include="pwiz\analysis\proteome_processing\ProteinList_Filter.hpp" />
     <ClInclude Include="pwiz\analysis\spectrum_processing\MS2Deisotoper.hpp" />
+    <ClInclude Include="pwiz\analysis\spectrum_processing\MS2NoiseFilter.hpp" />
     <ClInclude Include="pwiz\analysis\spectrum_processing\SpectrumList_3D.hpp" />
     <ClInclude Include="pwiz\analysis\spectrum_processing\SpectrumList_ChargeFromIsotope.hpp" />
+    <ClInclude Include="pwiz\analysis\spectrum_processing\SpectrumList_Demux.hpp" />
     <ClInclude Include="pwiz\analysis\spectrum_processing\SpectrumList_DiaUmpire.hpp" />
     <ClInclude Include="pwiz\analysis\spectrum_processing\SpectrumList_IonMobility.hpp" />
     <ClInclude Include="pwiz\analysis\spectrum_processing\SpectrumList_LockmassRefiner.hpp" />
@@ -925,6 +951,12 @@
     <ClInclude Include="pwiz\data\msdata\ChromatogramList_mz5.hpp" />
     <ClInclude Include="pwiz\data\msdata\Index_mzML.hpp" />
     <ClInclude Include="pwiz\data\msdata\MSNumpress.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\Configuration_mz5.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\Connection_mz5.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\Datastructures_mz5.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\ReferenceRead_mz5.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\ReferenceWrite_mz5.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\Translator_mz5.hpp" />
     <ClInclude Include="pwiz\data\msdata\Serializer_MSn.hpp" />
     <ClInclude Include="pwiz\data\msdata\Serializer_mz5.hpp" />
     <ClInclude Include="pwiz\data\msdata\SpectrumList_MSn.hpp" />
@@ -944,8 +976,10 @@
     <ClInclude Include="pwiz\data\vendor_readers\Shimadzu\ChromatogramList_Shimadzu.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\Shimadzu\Reader_Shimadzu.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\Shimadzu\SpectrumList_Shimadzu.hpp" />
+    <ClInclude Include="pwiz\data\vendor_readers\UIMF\ChromatogramList_UIMF.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\UIMF\Reader_UIMF.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\UIMF\SpectrumList_UIMF.hpp" />
+    <ClInclude Include="pwiz\data\vendor_readers\UNIFI\ChromatogramList_UNIFI.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\UNIFI\Reader_UNIFI.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\UNIFI\Reader_UNIFI_Detail.hpp" />
     <ClInclude Include="pwiz\data\vendor_readers\UNIFI\SpectrumList_UNIFI.hpp" />
@@ -955,6 +989,7 @@
     <ClInclude Include="pwiz\data\vendor_readers\Waters\SpectrumList_Waters.hpp" />
     <ClInclude Include="pwiz\utility\bindings\CLI\analysis\spectrum_processing.hpp" />
     <ClInclude Include="pwiz\utility\bindings\CLI\chemistry\chemistry.hpp" />
+    <ClInclude Include="pwiz\utility\bindings\CLI\common\BinaryData.hpp" />
     <ClInclude Include="pwiz\utility\bindings\CLI\common\cv.hpp" />
     <ClInclude Include="pwiz\utility\bindings\CLI\common\IterationListener.hpp" />
     <ClInclude Include="pwiz\utility\bindings\CLI\common\map.hpp" />
@@ -997,6 +1032,7 @@
     <ClInclude Include="pwiz\utility\bindings\CLI\tradata\Reader.hpp" />
     <ClInclude Include="pwiz\utility\bindings\CLI\tradata\TraData.hpp" />
     <ClInclude Include="pwiz\utility\bindings\CLI\tradata\TraDataFile.hpp" />
+    <ClInclude Include="pwiz\utility\chemistry\MzMobilityWindow.hpp" />
     <ClInclude Include="pwiz\utility\misc\BinaryData.hpp" />
     <ClInclude Include="pwiz\utility\misc\sort_together.hpp" />
     <ClInclude Include="pwiz\utility\misc\std.hpp" />
@@ -1330,6 +1366,7 @@
   <ItemGroup>
     <None Include="Jamroot.jam" />
     <None Include="libraries\boost-build\src\tools\msvc.jam" />
+    <None Include="pwiz\data\common\cv.inl" />
     <None Include="scripts\wix\pwiz-setup.py" />
     <None Include="scripts\wix\pwiz-setup.wxs.template" />
     <None Include="scripts\wix\vendor-dlls.wxs-fragment" />

diff --git a/pwiz.vcxproj.filters b/pwiz.vcxproj.filters
@@ -567,6 +567,30 @@
     <ClCompile Include="pwiz_aux\msrc\utility\vendor_api\UIMF\UIMFReaderTest.cpp" />
     <ClCompile Include="pwiz\analysis\dia_umpire\DiaUmpire.cpp" />
     <ClCompile Include="pwiz\analysis\dia_umpire\IsotopePatternMap.cpp" />
+    <ClCompile Include="pwiz\analysis\spectrum_processing\SpectrumList_DiaUmpire.cpp" />
+    <ClCompile Include="pwiz\analysis\spectrum_processing\SpectrumList_DiaUmpireTest.cpp" />
+    <ClCompile Include="pwiz\utility\bindings\CLI\timstof_prm_scheduler\PrmScheduler.cpp" />
+    <ClCompile Include="pwiz\utility\bindings\CLI\timstof_prm_scheduler\PrmSchedulerTest.cpp" />
+    <ClCompile Include="pwiz\analysis\common\CwtPeakDetectorTest.cpp" />
+    <ClCompile Include="pwiz\analysis\common\CwtPeakDetector.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramList_Filter.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramList_FilterTest.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramList_LockmassRefiner.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramList_LockmassRefinerTest.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramListFactoryTest.cpp" />
+    <ClCompile Include="pwiz\analysis\chromatogram_processing\ChromatogramListFactory.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\Configuration_mz5.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\Connection_mz5.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\Datastructures_mz5.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\ReferenceRead_mz5.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\ReferenceWrite_mz5.cpp" />
+    <ClCompile Include="pwiz\data\msdata\mz5\Translator_mz5.cpp" />
+    <ClCompile Include="pwiz\data\msdata\SpectrumListBase.cpp" />
+    <ClCompile Include="pwiz\data\vendor_readers\UIMF\ChromatogramList_UIMF.cpp" />
+    <ClCompile Include="pwiz\data\vendor_readers\UNIFI\ChromatogramList_UNIFI.cpp" />
+    <ClCompile Include="pwiz\utility\bindings\CLI\analysis\SpectrumList_IonMobility_Test.cpp" />
+    <ClCompile Include="pwiz\utility\misc\String.cpp" />
+    <ClCompile Include="pwiz_tools\commandline\idcat.cpp" />
   </ItemGroup>
   <ItemGroup>
     <ClInclude Include="libraries\boost_aux\boost\nowide\args.hpp" />
@@ -1008,12 +1032,43 @@
     <ClInclude Include="pwiz\analysis\dia_umpire\PeakCluster.hpp" />
     <ClInclude Include="pwiz\analysis\dia_umpire\PeakCurve.hpp" />
     <ClInclude Include="pwiz\analysis\dia_umpire\ScanData.hpp" />
+    <ClInclude Include="pwiz\analysis\spectrum_processing\SpectrumList_DiaUmpire.hpp" />
+    <ClInclude Include="pwiz\utility\bindings\CLI\timstof_prm_scheduler\prmscheduler.h" />
+    <ClInclude Include="pwiz\utility\bindings\CLI\timstof_prm_scheduler\PrmScheduler.hpp" />
+    <ClInclude Include="pwiz\utility\misc\sort_together.hpp" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Mobilion\MBICalibration.h" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Mobilion\MBICollection.h" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Mobilion\MBIConstants.h" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Mobilion\MBIFile.h" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Mobilion\MBIFrame.h" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Mobilion\MBIGate.h" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Mobilion\MBIMetadata.h" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Mobilion\MBIScan.h" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Mobilion\MBIUtils.h" />
+    <ClInclude Include="pwiz_aux\msrc\utility\vendor_api\Waters\WatersRawFile.hpp" />
+    <ClInclude Include="pwiz\analysis\common\CwtPeakDetector.hpp" />
+    <ClInclude Include="pwiz\analysis\chromatogram_processing\ChromatogramList_Filter.hpp" />
+    <ClInclude Include="pwiz\analysis\chromatogram_processing\ChromatogramList_LockmassRefiner.hpp" />
+    <ClInclude Include="pwiz\analysis\chromatogram_processing\ChromatogramListFactory.hpp" />
+    <ClInclude Include="pwiz\analysis\spectrum_processing\SpectrumList_Demux.hpp" />
+    <ClInclude Include="pwiz\analysis\spectrum_processing\MS2NoiseFilter.hpp" />
+    <ClInclude Include="pwiz\utility\chemistry\MzMobilityWindow.hpp" />
+    <ClInclude Include="pwiz\utility\bindings\CLI\common\BinaryData.hpp" />
+    <ClInclude Include="pwiz\data\vendor_readers\UNIFI\ChromatogramList_UNIFI.hpp" />
+    <ClInclude Include="pwiz\data\vendor_readers\UIMF\ChromatogramList_UIMF.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\Translator_mz5.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\ReferenceWrite_mz5.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\ReferenceRead_mz5.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\Datastructures_mz5.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\Connection_mz5.hpp" />
+    <ClInclude Include="pwiz\data\msdata\mz5\Configuration_mz5.hpp" />
   </ItemGroup>
   <ItemGroup>
     <None Include="Jamroot.jam" />
     <None Include="scripts\wix\vendor-dlls.wxs-fragment" />
     <None Include="scripts\wix\pwiz-setup.py" />
     <None Include="scripts\wix\pwiz-setup.wxs.template" />
     <None Include="libraries\boost-build\src\tools\msvc.jam" />
+    <None Include="pwiz\data\common\cv.inl" />
   </ItemGroup>
 </Project>
diff --git a/pwiz/analysis/dia_umpire/ScanData.hpp b/pwiz/analysis/dia_umpire/ScanData.hpp
@@ -35,6 +35,7 @@
 #include "pwiz/data/common/cv.hpp"
 #include "pwiz/data/msdata/MSData.hpp"
 #include "pwiz/utility/chemistry/Chemistry.hpp"
+#include "pwiz/utility/misc/sort_together.hpp"
 
 
 namespace DiaUmpire {
@@ -670,8 +671,12 @@ class ScanCollection
         scan.RetentionTime = spectrum->scanList.scans.at(0).cvParam(MS_scan_start_time).timeInSeconds() / 60;
         scan.centroided = spectrum->hasCVParam(MS_centroid_spectrum);
 
-        const auto& mzArray = spectrum->getMZArray()->data;
-        const auto& intensityArray = spectrum->getIntensityArray()->data;
+        // local array copies
+        vector<double> mzArray(spectrum->getMZArray()->data);
+        vector<double> intensityArray(spectrum->getIntensityArray()->data);
+
+        pwiz::util::sort_together(mzArray, intensityArray); // ensure data is m/z sorted
+
         for (size_t i = 0; i < mzArray.size(); ++i)
             scan.AddPoint(mzArray[i], intensityArray[i]);
         NumPeaks += mzArray.size();