From f6d869b9b1e169705e28c2ed2df2971e051c54f2 Mon Sep 17 00:00:00 2001
From: stepa <stepa@ARES>
Date: Wed, 15 Mar 2017 17:31:33 -0500
Subject: [PATCH 1/3] move stuff

---
 Benchmark/Benchmark.csproj                    |  35 ++---
 .../MzML => Benchmark}/packages.config        |   0
 .../ChemicalFormula.cs                        |   0
 .../Chemistry => Chemistry}/Chemistry.csproj  |   9 ++
 .../Chemistry => Chemistry}/Chemistry.nuspec  |   0
 .../ClassExtensions.cs                        |   0
 {mzLib/Chemistry => Chemistry}/Constants.cs   |   0
 {mzLib/Chemistry => Chemistry}/Element.cs     |   0
 .../Interfaces/IHasChemicalFormula.cs         |   0
 .../Interfaces/IHasMass.cs                    |   0
 {mzLib/Chemistry => Chemistry}/Isotope.cs     |   0
 .../IsotopicDistribution.cs                   |   0
 .../Chemistry => Chemistry}/PeriodicTable.cs  |   0
 .../Properties/AssemblyInfo.cs                |   0
 .../packages.config                           |   0
 .../AssemblyInfo.cpp                          |   0
 .../ClassLibrary1.cpp                         |   0
 .../ClassLibrary1.h                           |   0
 .../ClassLibrary1.vcxproj                     |   3 +-
 .../ClassLibrary1.vcxproj.filters             |   0
 .../Stdafx.cpp                                |   0
 .../Stdafx.h                                  |   0
 .../Win32Project8.h                           |   0
 .../app.ico                                   | Bin
 .../app.rc                                    | Bin
 .../resource.h                                |   0
 .../Chromatogram/Chromatogram.cs              |   0
 .../ChromatographicElutionProfile.cs          |   0
 .../Chromatogram/ChromatographicPeak.cs       |   0
 .../DataScan/IMsDataScan.cs                   |   0
 .../DataScan/IMsDataScanWithPrecursor.cs      |   0
 .../DataScan/MsDataScan.cs                    |   0
 .../DataScan/MsDataScanWithPrecursor.cs       |   0
 .../Enums/DissociationType.cs                 |   0
 .../Enums/MzAnalyzerType.cs                   |   0
 .../Enums/Polarity.cs                         |   0
 .../Enums/SmoothingType.cs                    |   0
 .../IIdentifications.cs                       |   0
 .../IMsDataFile.cs                            |   0
 .../IMsDynamicDataFile.cs                     |   0
 .../IMsStaticDataFile.cs                      |   0
 .../MassSpectrometry.csproj                   |   2 +-
 .../MsDataFile.cs                             |   0
 .../MzSpectra/IMzPeak.cs                      |   0
 .../MzSpectra/IMzSpectrum.cs                  |   0
 .../MzSpectra/MzPeak.cs                       |   0
 .../MzSpectra/MzSpectrum.cs                   |   0
 .../Properties/AssemblyInfo.cs                |   0
 MzLibUtil/MzLibUtil.csproj                    |   9 ++
 {mzLib/Spectra => MzLibUtil}/packages.config  |   1 +
 .../MassSpecFiles/MzML => MzML}/IMzmlScan.cs  |   0
 .../MassSpecFiles/MzML => MzML}/MzML.csproj   |  14 +-
 {mzLib/MassSpecFiles/MzML => MzML}/Mzml.cs    |   0
 .../MzML => MzML}/MzmlMethods.cs              |   0
 .../MassSpecFiles/MzML => MzML}/MzmlPeak.cs   |   0
 .../MassSpecFiles/MzML => MzML}/MzmlScan.cs   |   0
 .../MzML => MzML}/MzmlScanWithPrecursor.cs    |   0
 .../MzML => MzML}/MzmlSpectrum.cs             |   0
 .../MzML => MzML}/Properties/AssemblyInfo.cs  |   0
 .../MzML => MzML}/XSD/mzML1_1_1_idx.cs        |   0
 .../MzML => MzML}/mzML1.1.0.designer.cs       |   0
 MzML/packages.config                          |   5 +
 .../AminoAcidPolymer.cs                       |   0
 .../ChemicalFormulaFragment.cs                |   0
 .../ChemicalFormulaModification.cs            |   0
 .../ChemicalFormulaTerminus.cs                |   0
 .../DatabaseReference.cs                      |   0
 .../DigestionPoint.cs                         |   0
 {mzLib/Proteomics => Proteomics}/Fragment.cs  |   0
 .../FragmentTypes.cs                          |   0
 .../Interfaces/IProtease.cs                   |   0
 .../Proteomics => Proteomics}/Modification.cs |   0
 .../ModificationCollection.cs                 |   0
 .../ModificationMotif.cs                      |   0
 .../ModificationSites.cs                      |   0
 .../ModificationWithLocation.cs               |   0
 .../ModificationWithMass.cs                   |   0
 .../ModificationWithMassAndCf.cs              |   0
 .../OldSchoolModification.cs                  |   0
 ...olModificationWithMultiplePossibilities.cs |   0
 {mzLib/Proteomics => Proteomics}/Peptide.cs   |   0
 .../Properties/AssemblyInfo.cs                |   0
 {mzLib/Proteomics => Proteomics}/Protein.cs   |   0
 .../ProteolysisProduct.cs                     |   0
 .../Proteomics.csproj                         |   2 +-
 .../Proteomics.nuspec                         |   0
 {mzLib/Proteomics => Proteomics}/Residue.cs   |   0
 {mzLib/Proteomics => Proteomics}/Terminus.cs  |   0
 .../Util/AminoAcidPolymerExtensions.cs        |   0
 {mzLib/Spectra => Spectra}/IPeak.cs           |   0
 {mzLib/Spectra => Spectra}/ISpectrum.cs       |   0
 {mzLib/Spectra => Spectra}/Peak.cs            |   0
 .../Properties/AssemblyInfo.cs                |   0
 {mzLib/Spectra => Spectra}/Spectra.csproj     |  14 +-
 {mzLib/Spectra => Spectra}/Spectrum.cs        |   0
 .../Thermo => Spectra}/packages.config        |   1 +
 Test/Test.csproj                              |  40 ++---
 Test/packages.config                          |   1 +
 TestThermo/TestThermo.csproj                  |  30 ++--
 TestThermo/packages.config                    |   2 +
 .../Thermo => Thermo}/IThermoScan.cs          |   0
 .../Properties/AssemblyInfo.cs                |   0
 .../Thermo => Thermo}/Thermo.csproj           |  19 ++-
 .../Thermo => Thermo}/ThermoDynamicData.cs    |   0
 .../Thermo => Thermo}/ThermoFile.cs           |   0
 .../Thermo => Thermo}/ThermoGlobalParams.cs   |   0
 .../Thermo => Thermo}/ThermoMzPeak.cs         |   0
 .../Thermo => Thermo}/ThermoReadException.cs  |   0
 .../Thermo => Thermo}/ThermoScan.cs           |   0
 .../ThermoScanWithPrecursor.cs                |   0
 .../Thermo => Thermo}/ThermoSpectrum.cs       |   0
 .../Thermo => Thermo}/ThermoStaticData.cs     |   0
 Thermo/packages.config                        |   4 +
 .../ReadMe.txt                                |   0
 .../Win32Project8.cpp                         |   0
 .../Win32Project8.h                           |   0
 .../Win32Project8.vcxproj                     |   0
 .../Win32Project8.vcxproj.filters             |   0
 .../dllmain.cpp                               |   0
 .../stdafx.cpp                                |   0
 .../stdafx.h                                  |   0
 .../targetver.h                               |   0
 .../Generated/PsiModGenerated.cs              |   0
 .../Generated/unimod_2.cs                     |   0
 .../Loaders.cs                                |   0
 .../PeriodicTableLoader.cs                    |   0
 .../Properties/AssemblyInfo.cs                |   0
 .../ProteinDbLoader.cs                        |   0
 .../ProteinDbWriter.cs                        |   0
 .../PtmListLoader.cs                          |   0
 .../PtmListLoaderException.cs                 |   0
 .../UnimodLoader.cs                           |   0
 .../UsefulProteomicsDatabases.csproj          |   8 +-
 .../UsefulProteomicsDatabases.nuspec          |   0
 UsefulProteomicsDatabases/packages.config     |   5 +
 .../MzidIdentifications.cs                    |   0
 .../Properties/AssemblyInfo.cs                |   0
 .../mzIdentML => mzIdentML}/mzIdentML.csproj  |   6 +-
 .../mzIdentML => mzIdentML}/mzIdentML1_1_0.cs |   0
 .../mzIdentML => mzIdentML}/mzIdentML1_1_1.cs |   0
 mzLib.nuspec                                  |   4 +-
 mzLib.sln                                     | 147 +++++++++++-------
 mzLib.targets                                 |   2 +-
 143 files changed, 214 insertions(+), 149 deletions(-)
 rename {mzLib/MassSpecFiles/MzML => Benchmark}/packages.config (100%)
 rename {mzLib/Chemistry => Chemistry}/ChemicalFormula.cs (100%)
 rename {mzLib/Chemistry => Chemistry}/Chemistry.csproj (84%)
 rename {mzLib/Chemistry => Chemistry}/Chemistry.nuspec (100%)
 rename {mzLib/Chemistry => Chemistry}/ClassExtensions.cs (100%)
 rename {mzLib/Chemistry => Chemistry}/Constants.cs (100%)
 rename {mzLib/Chemistry => Chemistry}/Element.cs (100%)
 rename {mzLib/Chemistry => Chemistry}/Interfaces/IHasChemicalFormula.cs (100%)
 rename {mzLib/Chemistry => Chemistry}/Interfaces/IHasMass.cs (100%)
 rename {mzLib/Chemistry => Chemistry}/Isotope.cs (100%)
 rename {mzLib/Chemistry => Chemistry}/IsotopicDistribution.cs (100%)
 rename {mzLib/Chemistry => Chemistry}/PeriodicTable.cs (100%)
 rename {mzLib/Chemistry => Chemistry}/Properties/AssemblyInfo.cs (100%)
 rename {mzLib/UsefulProteomicsDatabases => Chemistry}/packages.config (100%)
 rename {ClassLibrary1 => ManagedThermoHelperLayer}/AssemblyInfo.cpp (100%)
 rename {ClassLibrary1 => ManagedThermoHelperLayer}/ClassLibrary1.cpp (100%)
 rename {ClassLibrary1 => ManagedThermoHelperLayer}/ClassLibrary1.h (100%)
 rename {ClassLibrary1 => ManagedThermoHelperLayer}/ClassLibrary1.vcxproj (96%)
 rename {ClassLibrary1 => ManagedThermoHelperLayer}/ClassLibrary1.vcxproj.filters (100%)
 rename {ClassLibrary1 => ManagedThermoHelperLayer}/Stdafx.cpp (100%)
 rename {ClassLibrary1 => ManagedThermoHelperLayer}/Stdafx.h (100%)
 rename {ClassLibrary1 => ManagedThermoHelperLayer}/Win32Project8.h (100%)
 rename {ClassLibrary1 => ManagedThermoHelperLayer}/app.ico (100%)
 rename {ClassLibrary1 => ManagedThermoHelperLayer}/app.rc (100%)
 rename {ClassLibrary1 => ManagedThermoHelperLayer}/resource.h (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/Chromatogram/Chromatogram.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/Chromatogram/ChromatographicElutionProfile.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/Chromatogram/ChromatographicPeak.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/DataScan/IMsDataScan.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/DataScan/IMsDataScanWithPrecursor.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/DataScan/MsDataScan.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/DataScan/MsDataScanWithPrecursor.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/Enums/DissociationType.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/Enums/MzAnalyzerType.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/Enums/Polarity.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/Enums/SmoothingType.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/IIdentifications.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/IMsDataFile.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/IMsDynamicDataFile.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/IMsStaticDataFile.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/MassSpectrometry.csproj (98%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/MsDataFile.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/MzSpectra/IMzPeak.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/MzSpectra/IMzSpectrum.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/MzSpectra/MzPeak.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/MzSpectra/MzSpectrum.cs (100%)
 rename {mzLib/MassSpectrometry => MassSpectrometry}/Properties/AssemblyInfo.cs (100%)
 rename {mzLib/Spectra => MzLibUtil}/packages.config (60%)
 rename {mzLib/MassSpecFiles/MzML => MzML}/IMzmlScan.cs (100%)
 rename {mzLib/MassSpecFiles/MzML => MzML}/MzML.csproj (85%)
 rename {mzLib/MassSpecFiles/MzML => MzML}/Mzml.cs (100%)
 rename {mzLib/MassSpecFiles/MzML => MzML}/MzmlMethods.cs (100%)
 rename {mzLib/MassSpecFiles/MzML => MzML}/MzmlPeak.cs (100%)
 rename {mzLib/MassSpecFiles/MzML => MzML}/MzmlScan.cs (100%)
 rename {mzLib/MassSpecFiles/MzML => MzML}/MzmlScanWithPrecursor.cs (100%)
 rename {mzLib/MassSpecFiles/MzML => MzML}/MzmlSpectrum.cs (100%)
 rename {mzLib/MassSpecFiles/MzML => MzML}/Properties/AssemblyInfo.cs (100%)
 rename {mzLib/MassSpecFiles/MzML => MzML}/XSD/mzML1_1_1_idx.cs (100%)
 rename {mzLib/MassSpecFiles/MzML => MzML}/mzML1.1.0.designer.cs (100%)
 create mode 100644 MzML/packages.config
 rename {mzLib/Proteomics => Proteomics}/AminoAcidPolymer.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/ChemicalFormulaFragment.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/ChemicalFormulaModification.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/ChemicalFormulaTerminus.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/DatabaseReference.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/DigestionPoint.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/Fragment.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/FragmentTypes.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/Interfaces/IProtease.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/Modification.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/ModificationCollection.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/ModificationMotif.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/ModificationSites.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/ModificationWithLocation.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/ModificationWithMass.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/ModificationWithMassAndCf.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/OldSchoolModification.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/OldSchoolModificationWithMultiplePossibilities.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/Peptide.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/Properties/AssemblyInfo.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/Protein.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/ProteolysisProduct.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/Proteomics.csproj (98%)
 rename {mzLib/Proteomics => Proteomics}/Proteomics.nuspec (100%)
 rename {mzLib/Proteomics => Proteomics}/Residue.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/Terminus.cs (100%)
 rename {mzLib/Proteomics => Proteomics}/Util/AminoAcidPolymerExtensions.cs (100%)
 rename {mzLib/Spectra => Spectra}/IPeak.cs (100%)
 rename {mzLib/Spectra => Spectra}/ISpectrum.cs (100%)
 rename {mzLib/Spectra => Spectra}/Peak.cs (100%)
 rename {mzLib/Spectra => Spectra}/Properties/AssemblyInfo.cs (100%)
 rename {mzLib/Spectra => Spectra}/Spectra.csproj (88%)
 rename {mzLib/Spectra => Spectra}/Spectrum.cs (100%)
 rename {mzLib/MassSpecFiles/Thermo => Spectra}/packages.config (62%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/IThermoScan.cs (100%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/Properties/AssemblyInfo.cs (100%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/Thermo.csproj (88%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/ThermoDynamicData.cs (100%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/ThermoFile.cs (100%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/ThermoGlobalParams.cs (100%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/ThermoMzPeak.cs (100%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/ThermoReadException.cs (100%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/ThermoScan.cs (100%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/ThermoScanWithPrecursor.cs (100%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/ThermoSpectrum.cs (100%)
 rename {mzLib/MassSpecFiles/Thermo => Thermo}/ThermoStaticData.cs (100%)
 create mode 100644 Thermo/packages.config
 rename {Win32Project8 => UnmanagedThermoHelperLayer}/ReadMe.txt (100%)
 rename {Win32Project8 => UnmanagedThermoHelperLayer}/Win32Project8.cpp (100%)
 rename {Win32Project8 => UnmanagedThermoHelperLayer}/Win32Project8.h (100%)
 rename {Win32Project8 => UnmanagedThermoHelperLayer}/Win32Project8.vcxproj (100%)
 rename {Win32Project8 => UnmanagedThermoHelperLayer}/Win32Project8.vcxproj.filters (100%)
 rename {Win32Project8 => UnmanagedThermoHelperLayer}/dllmain.cpp (100%)
 rename {Win32Project8 => UnmanagedThermoHelperLayer}/stdafx.cpp (100%)
 rename {Win32Project8 => UnmanagedThermoHelperLayer}/stdafx.h (100%)
 rename {Win32Project8 => UnmanagedThermoHelperLayer}/targetver.h (100%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/Generated/PsiModGenerated.cs (100%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/Generated/unimod_2.cs (100%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/Loaders.cs (100%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/PeriodicTableLoader.cs (100%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/Properties/AssemblyInfo.cs (100%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/ProteinDbLoader.cs (100%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/ProteinDbWriter.cs (100%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/PtmListLoader.cs (100%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/PtmListLoaderException.cs (100%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/UnimodLoader.cs (100%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/UsefulProteomicsDatabases.csproj (90%)
 rename {mzLib/UsefulProteomicsDatabases => UsefulProteomicsDatabases}/UsefulProteomicsDatabases.nuspec (100%)
 create mode 100644 UsefulProteomicsDatabases/packages.config
 rename {mzLib/MassSpecFiles/mzIdentML => mzIdentML}/MzidIdentifications.cs (100%)
 rename {mzLib/MassSpecFiles/mzIdentML => mzIdentML}/Properties/AssemblyInfo.cs (100%)
 rename {mzLib/MassSpecFiles/mzIdentML => mzIdentML}/mzIdentML.csproj (93%)
 rename {mzLib/MassSpecFiles/mzIdentML => mzIdentML}/mzIdentML1_1_0.cs (100%)
 rename {mzLib/MassSpecFiles/mzIdentML => mzIdentML}/mzIdentML1_1_1.cs (100%)

diff --git a/Benchmark/Benchmark.csproj b/Benchmark/Benchmark.csproj
index 5383ed23a..c08367f9a 100644
--- a/Benchmark/Benchmark.csproj
+++ b/Benchmark/Benchmark.csproj
@@ -51,6 +51,9 @@
     <Prefer32Bit>true</Prefer32Bit>
   </PropertyGroup>
   <ItemGroup>
+    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
+    </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
     <Reference Include="System.Xml.Linq" />
@@ -59,6 +62,9 @@
     <Reference Include="System.Data" />
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
+    <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
+    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="Program.cs" />
@@ -66,6 +72,7 @@
   </ItemGroup>
   <ItemGroup>
     <None Include="App.config" />
+    <None Include="packages.config" />
     <None Include="yeast_160126.xml.gz">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
@@ -83,38 +90,22 @@
     </BootstrapperPackage>
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\mzLib\Chemistry\Chemistry.csproj">
+    <WCFMetadata Include="Service References\" />
+  </ItemGroup>
+  <ItemGroup>
+    <ProjectReference Include="..\Chemistry\Chemistry.csproj">
       <Project>{cbe368bb-fc84-458d-8099-87a63d17aa3b}</Project>
       <Name>Chemistry</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpecFiles\MzML\MzML.csproj">
-      <Project>{012434FB-88A9-4DEC-B887-5F64C0B481D4}</Project>
-      <Name>MzML</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpecFiles\Thermo\Thermo.csproj">
-      <Project>{24DC85FF-E97B-4140-9614-77DD8FDDD32F}</Project>
-      <Name>Thermo</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpectrometry\MassSpectrometry.csproj">
-      <Project>{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}</Project>
-      <Name>MassSpectrometry</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\Proteomics\Proteomics.csproj">
+    <ProjectReference Include="..\Proteomics\Proteomics.csproj">
       <Project>{4ab6ba94-b70c-4570-9ea6-165746d5b8e8}</Project>
       <Name>Proteomics</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\Spectra\Spectra.csproj">
-      <Project>{088e4fcb-d580-4bad-a811-a1796a7666d2}</Project>
-      <Name>Spectra</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\UsefulProteomicsDatabases\UsefulProteomicsDatabases.csproj">
+    <ProjectReference Include="..\UsefulProteomicsDatabases\UsefulProteomicsDatabases.csproj">
       <Project>{16f857b5-4942-4fa2-b198-bd4d14c1b2e4}</Project>
       <Name>UsefulProteomicsDatabases</Name>
     </ProjectReference>
   </ItemGroup>
-  <ItemGroup>
-    <WCFMetadata Include="Service References\" />
-  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <PropertyGroup>
     <PreBuildEvent>xcopy /y /d  "$(SolutionDir)x64\$(Configuration)\*.dll" "$(ProjectDir)$(OutDir)"</PreBuildEvent>
diff --git a/mzLib/MassSpecFiles/MzML/packages.config b/Benchmark/packages.config
similarity index 100%
rename from mzLib/MassSpecFiles/MzML/packages.config
rename to Benchmark/packages.config
diff --git a/mzLib/Chemistry/ChemicalFormula.cs b/Chemistry/ChemicalFormula.cs
similarity index 100%
rename from mzLib/Chemistry/ChemicalFormula.cs
rename to Chemistry/ChemicalFormula.cs
diff --git a/mzLib/Chemistry/Chemistry.csproj b/Chemistry/Chemistry.csproj
similarity index 84%
rename from mzLib/Chemistry/Chemistry.csproj
rename to Chemistry/Chemistry.csproj
index fb5ceae99..387bc584b 100644
--- a/mzLib/Chemistry/Chemistry.csproj
+++ b/Chemistry/Chemistry.csproj
@@ -37,6 +37,9 @@
     <SignAssembly>false</SignAssembly>
   </PropertyGroup>
   <ItemGroup>
+    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
+    </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
     <Reference Include="System.Xml.Linq" />
@@ -45,6 +48,9 @@
     <Reference Include="System.Data" />
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
+    <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
+    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="ChemicalFormula.cs" />
@@ -60,6 +66,9 @@
       <SonarQubeExclude>true</SonarQubeExclude>
     </Compile>
   </ItemGroup>
+  <ItemGroup>
+    <None Include="packages.config" />
+  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.
diff --git a/mzLib/Chemistry/Chemistry.nuspec b/Chemistry/Chemistry.nuspec
similarity index 100%
rename from mzLib/Chemistry/Chemistry.nuspec
rename to Chemistry/Chemistry.nuspec
diff --git a/mzLib/Chemistry/ClassExtensions.cs b/Chemistry/ClassExtensions.cs
similarity index 100%
rename from mzLib/Chemistry/ClassExtensions.cs
rename to Chemistry/ClassExtensions.cs
diff --git a/mzLib/Chemistry/Constants.cs b/Chemistry/Constants.cs
similarity index 100%
rename from mzLib/Chemistry/Constants.cs
rename to Chemistry/Constants.cs
diff --git a/mzLib/Chemistry/Element.cs b/Chemistry/Element.cs
similarity index 100%
rename from mzLib/Chemistry/Element.cs
rename to Chemistry/Element.cs
diff --git a/mzLib/Chemistry/Interfaces/IHasChemicalFormula.cs b/Chemistry/Interfaces/IHasChemicalFormula.cs
similarity index 100%
rename from mzLib/Chemistry/Interfaces/IHasChemicalFormula.cs
rename to Chemistry/Interfaces/IHasChemicalFormula.cs
diff --git a/mzLib/Chemistry/Interfaces/IHasMass.cs b/Chemistry/Interfaces/IHasMass.cs
similarity index 100%
rename from mzLib/Chemistry/Interfaces/IHasMass.cs
rename to Chemistry/Interfaces/IHasMass.cs
diff --git a/mzLib/Chemistry/Isotope.cs b/Chemistry/Isotope.cs
similarity index 100%
rename from mzLib/Chemistry/Isotope.cs
rename to Chemistry/Isotope.cs
diff --git a/mzLib/Chemistry/IsotopicDistribution.cs b/Chemistry/IsotopicDistribution.cs
similarity index 100%
rename from mzLib/Chemistry/IsotopicDistribution.cs
rename to Chemistry/IsotopicDistribution.cs
diff --git a/mzLib/Chemistry/PeriodicTable.cs b/Chemistry/PeriodicTable.cs
similarity index 100%
rename from mzLib/Chemistry/PeriodicTable.cs
rename to Chemistry/PeriodicTable.cs
diff --git a/mzLib/Chemistry/Properties/AssemblyInfo.cs b/Chemistry/Properties/AssemblyInfo.cs
similarity index 100%
rename from mzLib/Chemistry/Properties/AssemblyInfo.cs
rename to Chemistry/Properties/AssemblyInfo.cs
diff --git a/mzLib/UsefulProteomicsDatabases/packages.config b/Chemistry/packages.config
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/packages.config
rename to Chemistry/packages.config
diff --git a/ClassLibrary1/AssemblyInfo.cpp b/ManagedThermoHelperLayer/AssemblyInfo.cpp
similarity index 100%
rename from ClassLibrary1/AssemblyInfo.cpp
rename to ManagedThermoHelperLayer/AssemblyInfo.cpp
diff --git a/ClassLibrary1/ClassLibrary1.cpp b/ManagedThermoHelperLayer/ClassLibrary1.cpp
similarity index 100%
rename from ClassLibrary1/ClassLibrary1.cpp
rename to ManagedThermoHelperLayer/ClassLibrary1.cpp
diff --git a/ClassLibrary1/ClassLibrary1.h b/ManagedThermoHelperLayer/ClassLibrary1.h
similarity index 100%
rename from ClassLibrary1/ClassLibrary1.h
rename to ManagedThermoHelperLayer/ClassLibrary1.h
diff --git a/ClassLibrary1/ClassLibrary1.vcxproj b/ManagedThermoHelperLayer/ClassLibrary1.vcxproj
similarity index 96%
rename from ClassLibrary1/ClassLibrary1.vcxproj
rename to ManagedThermoHelperLayer/ClassLibrary1.vcxproj
index bfaf3b1bb..f20b1fa70 100644
--- a/ClassLibrary1/ClassLibrary1.vcxproj
+++ b/ManagedThermoHelperLayer/ClassLibrary1.vcxproj
@@ -99,9 +99,8 @@
     <Image Include="app.ico" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\Win32Project8\Win32Project8.vcxproj">
+    <ProjectReference Include="..\UnmanagedThermoHelperLayer\Win32Project8.vcxproj">
       <Project>{8913a108-5d93-4af7-b273-89a06e817611}</Project>
-      <CopyLocalSatelliteAssemblies>true</CopyLocalSatelliteAssemblies>
     </ProjectReference>
   </ItemGroup>
   <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
diff --git a/ClassLibrary1/ClassLibrary1.vcxproj.filters b/ManagedThermoHelperLayer/ClassLibrary1.vcxproj.filters
similarity index 100%
rename from ClassLibrary1/ClassLibrary1.vcxproj.filters
rename to ManagedThermoHelperLayer/ClassLibrary1.vcxproj.filters
diff --git a/ClassLibrary1/Stdafx.cpp b/ManagedThermoHelperLayer/Stdafx.cpp
similarity index 100%
rename from ClassLibrary1/Stdafx.cpp
rename to ManagedThermoHelperLayer/Stdafx.cpp
diff --git a/ClassLibrary1/Stdafx.h b/ManagedThermoHelperLayer/Stdafx.h
similarity index 100%
rename from ClassLibrary1/Stdafx.h
rename to ManagedThermoHelperLayer/Stdafx.h
diff --git a/ClassLibrary1/Win32Project8.h b/ManagedThermoHelperLayer/Win32Project8.h
similarity index 100%
rename from ClassLibrary1/Win32Project8.h
rename to ManagedThermoHelperLayer/Win32Project8.h
diff --git a/ClassLibrary1/app.ico b/ManagedThermoHelperLayer/app.ico
similarity index 100%
rename from ClassLibrary1/app.ico
rename to ManagedThermoHelperLayer/app.ico
diff --git a/ClassLibrary1/app.rc b/ManagedThermoHelperLayer/app.rc
similarity index 100%
rename from ClassLibrary1/app.rc
rename to ManagedThermoHelperLayer/app.rc
diff --git a/ClassLibrary1/resource.h b/ManagedThermoHelperLayer/resource.h
similarity index 100%
rename from ClassLibrary1/resource.h
rename to ManagedThermoHelperLayer/resource.h
diff --git a/mzLib/MassSpectrometry/Chromatogram/Chromatogram.cs b/MassSpectrometry/Chromatogram/Chromatogram.cs
similarity index 100%
rename from mzLib/MassSpectrometry/Chromatogram/Chromatogram.cs
rename to MassSpectrometry/Chromatogram/Chromatogram.cs
diff --git a/mzLib/MassSpectrometry/Chromatogram/ChromatographicElutionProfile.cs b/MassSpectrometry/Chromatogram/ChromatographicElutionProfile.cs
similarity index 100%
rename from mzLib/MassSpectrometry/Chromatogram/ChromatographicElutionProfile.cs
rename to MassSpectrometry/Chromatogram/ChromatographicElutionProfile.cs
diff --git a/mzLib/MassSpectrometry/Chromatogram/ChromatographicPeak.cs b/MassSpectrometry/Chromatogram/ChromatographicPeak.cs
similarity index 100%
rename from mzLib/MassSpectrometry/Chromatogram/ChromatographicPeak.cs
rename to MassSpectrometry/Chromatogram/ChromatographicPeak.cs
diff --git a/mzLib/MassSpectrometry/DataScan/IMsDataScan.cs b/MassSpectrometry/DataScan/IMsDataScan.cs
similarity index 100%
rename from mzLib/MassSpectrometry/DataScan/IMsDataScan.cs
rename to MassSpectrometry/DataScan/IMsDataScan.cs
diff --git a/mzLib/MassSpectrometry/DataScan/IMsDataScanWithPrecursor.cs b/MassSpectrometry/DataScan/IMsDataScanWithPrecursor.cs
similarity index 100%
rename from mzLib/MassSpectrometry/DataScan/IMsDataScanWithPrecursor.cs
rename to MassSpectrometry/DataScan/IMsDataScanWithPrecursor.cs
diff --git a/mzLib/MassSpectrometry/DataScan/MsDataScan.cs b/MassSpectrometry/DataScan/MsDataScan.cs
similarity index 100%
rename from mzLib/MassSpectrometry/DataScan/MsDataScan.cs
rename to MassSpectrometry/DataScan/MsDataScan.cs
diff --git a/mzLib/MassSpectrometry/DataScan/MsDataScanWithPrecursor.cs b/MassSpectrometry/DataScan/MsDataScanWithPrecursor.cs
similarity index 100%
rename from mzLib/MassSpectrometry/DataScan/MsDataScanWithPrecursor.cs
rename to MassSpectrometry/DataScan/MsDataScanWithPrecursor.cs
diff --git a/mzLib/MassSpectrometry/Enums/DissociationType.cs b/MassSpectrometry/Enums/DissociationType.cs
similarity index 100%
rename from mzLib/MassSpectrometry/Enums/DissociationType.cs
rename to MassSpectrometry/Enums/DissociationType.cs
diff --git a/mzLib/MassSpectrometry/Enums/MzAnalyzerType.cs b/MassSpectrometry/Enums/MzAnalyzerType.cs
similarity index 100%
rename from mzLib/MassSpectrometry/Enums/MzAnalyzerType.cs
rename to MassSpectrometry/Enums/MzAnalyzerType.cs
diff --git a/mzLib/MassSpectrometry/Enums/Polarity.cs b/MassSpectrometry/Enums/Polarity.cs
similarity index 100%
rename from mzLib/MassSpectrometry/Enums/Polarity.cs
rename to MassSpectrometry/Enums/Polarity.cs
diff --git a/mzLib/MassSpectrometry/Enums/SmoothingType.cs b/MassSpectrometry/Enums/SmoothingType.cs
similarity index 100%
rename from mzLib/MassSpectrometry/Enums/SmoothingType.cs
rename to MassSpectrometry/Enums/SmoothingType.cs
diff --git a/mzLib/MassSpectrometry/IIdentifications.cs b/MassSpectrometry/IIdentifications.cs
similarity index 100%
rename from mzLib/MassSpectrometry/IIdentifications.cs
rename to MassSpectrometry/IIdentifications.cs
diff --git a/mzLib/MassSpectrometry/IMsDataFile.cs b/MassSpectrometry/IMsDataFile.cs
similarity index 100%
rename from mzLib/MassSpectrometry/IMsDataFile.cs
rename to MassSpectrometry/IMsDataFile.cs
diff --git a/mzLib/MassSpectrometry/IMsDynamicDataFile.cs b/MassSpectrometry/IMsDynamicDataFile.cs
similarity index 100%
rename from mzLib/MassSpectrometry/IMsDynamicDataFile.cs
rename to MassSpectrometry/IMsDynamicDataFile.cs
diff --git a/mzLib/MassSpectrometry/IMsStaticDataFile.cs b/MassSpectrometry/IMsStaticDataFile.cs
similarity index 100%
rename from mzLib/MassSpectrometry/IMsStaticDataFile.cs
rename to MassSpectrometry/IMsStaticDataFile.cs
diff --git a/mzLib/MassSpectrometry/MassSpectrometry.csproj b/MassSpectrometry/MassSpectrometry.csproj
similarity index 98%
rename from mzLib/MassSpectrometry/MassSpectrometry.csproj
rename to MassSpectrometry/MassSpectrometry.csproj
index bdc63cdfb..4c64ab9a3 100644
--- a/mzLib/MassSpectrometry/MassSpectrometry.csproj
+++ b/MassSpectrometry/MassSpectrometry.csproj
@@ -68,7 +68,7 @@
     <Compile Include="Enums\SmoothingType.cs" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\..\MzLibUtil\MzLibUtil.csproj">
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}</Project>
       <Name>MzLibUtil</Name>
     </ProjectReference>
diff --git a/mzLib/MassSpectrometry/MsDataFile.cs b/MassSpectrometry/MsDataFile.cs
similarity index 100%
rename from mzLib/MassSpectrometry/MsDataFile.cs
rename to MassSpectrometry/MsDataFile.cs
diff --git a/mzLib/MassSpectrometry/MzSpectra/IMzPeak.cs b/MassSpectrometry/MzSpectra/IMzPeak.cs
similarity index 100%
rename from mzLib/MassSpectrometry/MzSpectra/IMzPeak.cs
rename to MassSpectrometry/MzSpectra/IMzPeak.cs
diff --git a/mzLib/MassSpectrometry/MzSpectra/IMzSpectrum.cs b/MassSpectrometry/MzSpectra/IMzSpectrum.cs
similarity index 100%
rename from mzLib/MassSpectrometry/MzSpectra/IMzSpectrum.cs
rename to MassSpectrometry/MzSpectra/IMzSpectrum.cs
diff --git a/mzLib/MassSpectrometry/MzSpectra/MzPeak.cs b/MassSpectrometry/MzSpectra/MzPeak.cs
similarity index 100%
rename from mzLib/MassSpectrometry/MzSpectra/MzPeak.cs
rename to MassSpectrometry/MzSpectra/MzPeak.cs
diff --git a/mzLib/MassSpectrometry/MzSpectra/MzSpectrum.cs b/MassSpectrometry/MzSpectra/MzSpectrum.cs
similarity index 100%
rename from mzLib/MassSpectrometry/MzSpectra/MzSpectrum.cs
rename to MassSpectrometry/MzSpectra/MzSpectrum.cs
diff --git a/mzLib/MassSpectrometry/Properties/AssemblyInfo.cs b/MassSpectrometry/Properties/AssemblyInfo.cs
similarity index 100%
rename from mzLib/MassSpectrometry/Properties/AssemblyInfo.cs
rename to MassSpectrometry/Properties/AssemblyInfo.cs
diff --git a/MzLibUtil/MzLibUtil.csproj b/MzLibUtil/MzLibUtil.csproj
index ceafa6110..ba18cd96a 100644
--- a/MzLibUtil/MzLibUtil.csproj
+++ b/MzLibUtil/MzLibUtil.csproj
@@ -31,6 +31,9 @@
     <CodeAnalysisRuleSet>MinimumRecommendedRules.ruleset</CodeAnalysisRuleSet>
   </PropertyGroup>
   <ItemGroup>
+    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
+    </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
     <Reference Include="System.Xml.Linq" />
@@ -39,6 +42,9 @@
     <Reference Include="System.Data" />
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
+    <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
+    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="ClassExtensions.cs" />
@@ -50,6 +56,9 @@
     <Compile Include="Tolerance.cs" />
     <Compile Include="ToleranceUnit.cs" />
   </ItemGroup>
+  <ItemGroup>
+    <None Include="packages.config" />
+  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.
diff --git a/mzLib/Spectra/packages.config b/MzLibUtil/packages.config
similarity index 60%
rename from mzLib/Spectra/packages.config
rename to MzLibUtil/packages.config
index 515ae03a4..bbe5322b0 100644
--- a/mzLib/Spectra/packages.config
+++ b/MzLibUtil/packages.config
@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
   <package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
+  <package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
 </packages>
\ No newline at end of file
diff --git a/mzLib/MassSpecFiles/MzML/IMzmlScan.cs b/MzML/IMzmlScan.cs
similarity index 100%
rename from mzLib/MassSpecFiles/MzML/IMzmlScan.cs
rename to MzML/IMzmlScan.cs
diff --git a/mzLib/MassSpecFiles/MzML/MzML.csproj b/MzML/MzML.csproj
similarity index 85%
rename from mzLib/MassSpecFiles/MzML/MzML.csproj
rename to MzML/MzML.csproj
index fcbd05c18..03c7e33db 100644
--- a/mzLib/MassSpecFiles/MzML/MzML.csproj
+++ b/MzML/MzML.csproj
@@ -34,17 +34,15 @@
     <CodeAnalysisRuleSet>MinimumRecommendedRules.ruleset</CodeAnalysisRuleSet>
   </PropertyGroup>
   <ItemGroup>
-    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\..\..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
-      <Private>True</Private>
+    <Reference Include="nunit.framework, Version=3.6.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
+      <HintPath>..\packages\NUnit.3.6.1\lib\net45\nunit.framework.dll</HintPath>
     </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
     <Reference Include="System.Numerics" />
     <Reference Include="System.Xml" />
     <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\..\..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
-      <Private>True</Private>
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
     </Reference>
   </ItemGroup>
   <ItemGroup>
@@ -64,15 +62,15 @@
     <None Include="packages.config" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\..\..\MzLibUtil\MzLibUtil.csproj">
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}</Project>
       <Name>MzLibUtil</Name>
     </ProjectReference>
-    <ProjectReference Include="..\..\MassSpectrometry\MassSpectrometry.csproj">
+    <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj">
       <Project>{6febb7ed-0be6-4493-817e-cefd4cbe61dd}</Project>
       <Name>MassSpectrometry</Name>
     </ProjectReference>
-    <ProjectReference Include="..\..\Spectra\Spectra.csproj">
+    <ProjectReference Include="..\Spectra\Spectra.csproj">
       <Project>{088e4fcb-d580-4bad-a811-a1796a7666d2}</Project>
       <Name>Spectra</Name>
     </ProjectReference>
diff --git a/mzLib/MassSpecFiles/MzML/Mzml.cs b/MzML/Mzml.cs
similarity index 100%
rename from mzLib/MassSpecFiles/MzML/Mzml.cs
rename to MzML/Mzml.cs
diff --git a/mzLib/MassSpecFiles/MzML/MzmlMethods.cs b/MzML/MzmlMethods.cs
similarity index 100%
rename from mzLib/MassSpecFiles/MzML/MzmlMethods.cs
rename to MzML/MzmlMethods.cs
diff --git a/mzLib/MassSpecFiles/MzML/MzmlPeak.cs b/MzML/MzmlPeak.cs
similarity index 100%
rename from mzLib/MassSpecFiles/MzML/MzmlPeak.cs
rename to MzML/MzmlPeak.cs
diff --git a/mzLib/MassSpecFiles/MzML/MzmlScan.cs b/MzML/MzmlScan.cs
similarity index 100%
rename from mzLib/MassSpecFiles/MzML/MzmlScan.cs
rename to MzML/MzmlScan.cs
diff --git a/mzLib/MassSpecFiles/MzML/MzmlScanWithPrecursor.cs b/MzML/MzmlScanWithPrecursor.cs
similarity index 100%
rename from mzLib/MassSpecFiles/MzML/MzmlScanWithPrecursor.cs
rename to MzML/MzmlScanWithPrecursor.cs
diff --git a/mzLib/MassSpecFiles/MzML/MzmlSpectrum.cs b/MzML/MzmlSpectrum.cs
similarity index 100%
rename from mzLib/MassSpecFiles/MzML/MzmlSpectrum.cs
rename to MzML/MzmlSpectrum.cs
diff --git a/mzLib/MassSpecFiles/MzML/Properties/AssemblyInfo.cs b/MzML/Properties/AssemblyInfo.cs
similarity index 100%
rename from mzLib/MassSpecFiles/MzML/Properties/AssemblyInfo.cs
rename to MzML/Properties/AssemblyInfo.cs
diff --git a/mzLib/MassSpecFiles/MzML/XSD/mzML1_1_1_idx.cs b/MzML/XSD/mzML1_1_1_idx.cs
similarity index 100%
rename from mzLib/MassSpecFiles/MzML/XSD/mzML1_1_1_idx.cs
rename to MzML/XSD/mzML1_1_1_idx.cs
diff --git a/mzLib/MassSpecFiles/MzML/mzML1.1.0.designer.cs b/MzML/mzML1.1.0.designer.cs
similarity index 100%
rename from mzLib/MassSpecFiles/MzML/mzML1.1.0.designer.cs
rename to MzML/mzML1.1.0.designer.cs
diff --git a/MzML/packages.config b/MzML/packages.config
new file mode 100644
index 000000000..cafbdeab9
--- /dev/null
+++ b/MzML/packages.config
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="utf-8"?>
+<packages>
+  <package id="NUnit" version="3.6.1" targetFramework="net451" />
+  <package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
+</packages>
\ No newline at end of file
diff --git a/mzLib/Proteomics/AminoAcidPolymer.cs b/Proteomics/AminoAcidPolymer.cs
similarity index 100%
rename from mzLib/Proteomics/AminoAcidPolymer.cs
rename to Proteomics/AminoAcidPolymer.cs
diff --git a/mzLib/Proteomics/ChemicalFormulaFragment.cs b/Proteomics/ChemicalFormulaFragment.cs
similarity index 100%
rename from mzLib/Proteomics/ChemicalFormulaFragment.cs
rename to Proteomics/ChemicalFormulaFragment.cs
diff --git a/mzLib/Proteomics/ChemicalFormulaModification.cs b/Proteomics/ChemicalFormulaModification.cs
similarity index 100%
rename from mzLib/Proteomics/ChemicalFormulaModification.cs
rename to Proteomics/ChemicalFormulaModification.cs
diff --git a/mzLib/Proteomics/ChemicalFormulaTerminus.cs b/Proteomics/ChemicalFormulaTerminus.cs
similarity index 100%
rename from mzLib/Proteomics/ChemicalFormulaTerminus.cs
rename to Proteomics/ChemicalFormulaTerminus.cs
diff --git a/mzLib/Proteomics/DatabaseReference.cs b/Proteomics/DatabaseReference.cs
similarity index 100%
rename from mzLib/Proteomics/DatabaseReference.cs
rename to Proteomics/DatabaseReference.cs
diff --git a/mzLib/Proteomics/DigestionPoint.cs b/Proteomics/DigestionPoint.cs
similarity index 100%
rename from mzLib/Proteomics/DigestionPoint.cs
rename to Proteomics/DigestionPoint.cs
diff --git a/mzLib/Proteomics/Fragment.cs b/Proteomics/Fragment.cs
similarity index 100%
rename from mzLib/Proteomics/Fragment.cs
rename to Proteomics/Fragment.cs
diff --git a/mzLib/Proteomics/FragmentTypes.cs b/Proteomics/FragmentTypes.cs
similarity index 100%
rename from mzLib/Proteomics/FragmentTypes.cs
rename to Proteomics/FragmentTypes.cs
diff --git a/mzLib/Proteomics/Interfaces/IProtease.cs b/Proteomics/Interfaces/IProtease.cs
similarity index 100%
rename from mzLib/Proteomics/Interfaces/IProtease.cs
rename to Proteomics/Interfaces/IProtease.cs
diff --git a/mzLib/Proteomics/Modification.cs b/Proteomics/Modification.cs
similarity index 100%
rename from mzLib/Proteomics/Modification.cs
rename to Proteomics/Modification.cs
diff --git a/mzLib/Proteomics/ModificationCollection.cs b/Proteomics/ModificationCollection.cs
similarity index 100%
rename from mzLib/Proteomics/ModificationCollection.cs
rename to Proteomics/ModificationCollection.cs
diff --git a/mzLib/Proteomics/ModificationMotif.cs b/Proteomics/ModificationMotif.cs
similarity index 100%
rename from mzLib/Proteomics/ModificationMotif.cs
rename to Proteomics/ModificationMotif.cs
diff --git a/mzLib/Proteomics/ModificationSites.cs b/Proteomics/ModificationSites.cs
similarity index 100%
rename from mzLib/Proteomics/ModificationSites.cs
rename to Proteomics/ModificationSites.cs
diff --git a/mzLib/Proteomics/ModificationWithLocation.cs b/Proteomics/ModificationWithLocation.cs
similarity index 100%
rename from mzLib/Proteomics/ModificationWithLocation.cs
rename to Proteomics/ModificationWithLocation.cs
diff --git a/mzLib/Proteomics/ModificationWithMass.cs b/Proteomics/ModificationWithMass.cs
similarity index 100%
rename from mzLib/Proteomics/ModificationWithMass.cs
rename to Proteomics/ModificationWithMass.cs
diff --git a/mzLib/Proteomics/ModificationWithMassAndCf.cs b/Proteomics/ModificationWithMassAndCf.cs
similarity index 100%
rename from mzLib/Proteomics/ModificationWithMassAndCf.cs
rename to Proteomics/ModificationWithMassAndCf.cs
diff --git a/mzLib/Proteomics/OldSchoolModification.cs b/Proteomics/OldSchoolModification.cs
similarity index 100%
rename from mzLib/Proteomics/OldSchoolModification.cs
rename to Proteomics/OldSchoolModification.cs
diff --git a/mzLib/Proteomics/OldSchoolModificationWithMultiplePossibilities.cs b/Proteomics/OldSchoolModificationWithMultiplePossibilities.cs
similarity index 100%
rename from mzLib/Proteomics/OldSchoolModificationWithMultiplePossibilities.cs
rename to Proteomics/OldSchoolModificationWithMultiplePossibilities.cs
diff --git a/mzLib/Proteomics/Peptide.cs b/Proteomics/Peptide.cs
similarity index 100%
rename from mzLib/Proteomics/Peptide.cs
rename to Proteomics/Peptide.cs
diff --git a/mzLib/Proteomics/Properties/AssemblyInfo.cs b/Proteomics/Properties/AssemblyInfo.cs
similarity index 100%
rename from mzLib/Proteomics/Properties/AssemblyInfo.cs
rename to Proteomics/Properties/AssemblyInfo.cs
diff --git a/mzLib/Proteomics/Protein.cs b/Proteomics/Protein.cs
similarity index 100%
rename from mzLib/Proteomics/Protein.cs
rename to Proteomics/Protein.cs
diff --git a/mzLib/Proteomics/ProteolysisProduct.cs b/Proteomics/ProteolysisProduct.cs
similarity index 100%
rename from mzLib/Proteomics/ProteolysisProduct.cs
rename to Proteomics/ProteolysisProduct.cs
diff --git a/mzLib/Proteomics/Proteomics.csproj b/Proteomics/Proteomics.csproj
similarity index 98%
rename from mzLib/Proteomics/Proteomics.csproj
rename to Proteomics/Proteomics.csproj
index fa77634d3..90943f8d3 100644
--- a/mzLib/Proteomics/Proteomics.csproj
+++ b/Proteomics/Proteomics.csproj
@@ -73,7 +73,7 @@
     <Compile Include="Terminus.cs" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\..\MzLibUtil\MzLibUtil.csproj">
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{b208ff5f-5a33-490d-9ddb-7c76f5600fc4}</Project>
       <Name>MzLibUtil</Name>
     </ProjectReference>
diff --git a/mzLib/Proteomics/Proteomics.nuspec b/Proteomics/Proteomics.nuspec
similarity index 100%
rename from mzLib/Proteomics/Proteomics.nuspec
rename to Proteomics/Proteomics.nuspec
diff --git a/mzLib/Proteomics/Residue.cs b/Proteomics/Residue.cs
similarity index 100%
rename from mzLib/Proteomics/Residue.cs
rename to Proteomics/Residue.cs
diff --git a/mzLib/Proteomics/Terminus.cs b/Proteomics/Terminus.cs
similarity index 100%
rename from mzLib/Proteomics/Terminus.cs
rename to Proteomics/Terminus.cs
diff --git a/mzLib/Proteomics/Util/AminoAcidPolymerExtensions.cs b/Proteomics/Util/AminoAcidPolymerExtensions.cs
similarity index 100%
rename from mzLib/Proteomics/Util/AminoAcidPolymerExtensions.cs
rename to Proteomics/Util/AminoAcidPolymerExtensions.cs
diff --git a/mzLib/Spectra/IPeak.cs b/Spectra/IPeak.cs
similarity index 100%
rename from mzLib/Spectra/IPeak.cs
rename to Spectra/IPeak.cs
diff --git a/mzLib/Spectra/ISpectrum.cs b/Spectra/ISpectrum.cs
similarity index 100%
rename from mzLib/Spectra/ISpectrum.cs
rename to Spectra/ISpectrum.cs
diff --git a/mzLib/Spectra/Peak.cs b/Spectra/Peak.cs
similarity index 100%
rename from mzLib/Spectra/Peak.cs
rename to Spectra/Peak.cs
diff --git a/mzLib/Spectra/Properties/AssemblyInfo.cs b/Spectra/Properties/AssemblyInfo.cs
similarity index 100%
rename from mzLib/Spectra/Properties/AssemblyInfo.cs
rename to Spectra/Properties/AssemblyInfo.cs
diff --git a/mzLib/Spectra/Spectra.csproj b/Spectra/Spectra.csproj
similarity index 88%
rename from mzLib/Spectra/Spectra.csproj
rename to Spectra/Spectra.csproj
index dff401754..654780c7e 100644
--- a/mzLib/Spectra/Spectra.csproj
+++ b/Spectra/Spectra.csproj
@@ -34,8 +34,10 @@
   </PropertyGroup>
   <ItemGroup>
     <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
-      <Private>True</Private>
+      <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
+    </Reference>
+    <Reference Include="nunit.framework, Version=3.6.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
+      <HintPath>..\packages\NUnit.3.6.1\lib\net45\nunit.framework.dll</HintPath>
     </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
@@ -56,14 +58,14 @@
     </Compile>
   </ItemGroup>
   <ItemGroup>
-    <None Include="packages.config" />
-  </ItemGroup>
-  <ItemGroup>
-    <ProjectReference Include="..\..\MzLibUtil\MzLibUtil.csproj">
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}</Project>
       <Name>MzLibUtil</Name>
     </ProjectReference>
   </ItemGroup>
+  <ItemGroup>
+    <None Include="packages.config" />
+  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.
diff --git a/mzLib/Spectra/Spectrum.cs b/Spectra/Spectrum.cs
similarity index 100%
rename from mzLib/Spectra/Spectrum.cs
rename to Spectra/Spectrum.cs
diff --git a/mzLib/MassSpecFiles/Thermo/packages.config b/Spectra/packages.config
similarity index 62%
rename from mzLib/MassSpecFiles/Thermo/packages.config
rename to Spectra/packages.config
index 515ae03a4..73e9079e5 100644
--- a/mzLib/MassSpecFiles/Thermo/packages.config
+++ b/Spectra/packages.config
@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
   <package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
+  <package id="NUnit" version="3.6.1" targetFramework="net451" />
 </packages>
\ No newline at end of file
diff --git a/Test/Test.csproj b/Test/Test.csproj
index 07f5507ff..3cee44fe1 100644
--- a/Test/Test.csproj
+++ b/Test/Test.csproj
@@ -29,7 +29,6 @@
   <ItemGroup>
     <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
       <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
-      <Private>True</Private>
     </Reference>
     <Reference Include="nunit.framework, Version=3.6.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
       <HintPath>..\packages\NUnit.3.6.1\lib\net45\nunit.framework.dll</HintPath>
@@ -43,6 +42,9 @@
     <Reference Include="System.Data" />
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
+    <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
+    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="FakeMsDataFile.cs" />
@@ -67,35 +69,35 @@
     <Compile Include="TestTolerance.cs" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
-      <Project>{b208ff5f-5a33-490d-9ddb-7c76f5600fc4}</Project>
-      <Name>MzLibUtil</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\Chemistry\Chemistry.csproj">
-      <Project>{CBE368BB-FC84-458D-8099-87A63D17AA3B}</Project>
+    <ProjectReference Include="..\Chemistry\Chemistry.csproj">
+      <Project>{cbe368bb-fc84-458d-8099-87a63d17aa3b}</Project>
       <Name>Chemistry</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpecFiles\mzIdentML\mzIdentML.csproj">
-      <Project>{63D869DF-55D8-4043-AD89-F90462403EBB}</Project>
+    <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj">
+      <Project>{6febb7ed-0be6-4493-817e-cefd4cbe61dd}</Project>
+      <Name>MassSpectrometry</Name>
+    </ProjectReference>
+    <ProjectReference Include="..\mzIdentML\mzIdentML.csproj">
+      <Project>{63d869df-55d8-4043-ad89-f90462403ebb}</Project>
       <Name>mzIdentML</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpecFiles\MzML\MzML.csproj">
-      <Project>{012434FB-88A9-4DEC-B887-5F64C0B481D4}</Project>
-      <Name>MzML</Name>
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
+      <Project>{b208ff5f-5a33-490d-9ddb-7c76f5600fc4}</Project>
+      <Name>MzLibUtil</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpectrometry\MassSpectrometry.csproj">
-      <Project>{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}</Project>
-      <Name>MassSpectrometry</Name>
+    <ProjectReference Include="..\MzML\MzML.csproj">
+      <Project>{012434fb-88a9-4dec-b887-5f64c0b481d4}</Project>
+      <Name>MzML</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\Proteomics\Proteomics.csproj">
-      <Project>{4AB6BA94-B70C-4570-9EA6-165746D5B8E8}</Project>
+    <ProjectReference Include="..\Proteomics\Proteomics.csproj">
+      <Project>{4ab6ba94-b70c-4570-9ea6-165746d5b8e8}</Project>
       <Name>Proteomics</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\Spectra\Spectra.csproj">
+    <ProjectReference Include="..\Spectra\Spectra.csproj">
       <Project>{088E4FCB-D580-4BAD-A811-A1796A7666D2}</Project>
       <Name>Spectra</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\UsefulProteomicsDatabases\UsefulProteomicsDatabases.csproj">
+    <ProjectReference Include="..\UsefulProteomicsDatabases\UsefulProteomicsDatabases.csproj">
       <Project>{16f857b5-4942-4fa2-b198-bd4d14c1b2e4}</Project>
       <Name>UsefulProteomicsDatabases</Name>
     </ProjectReference>
diff --git a/Test/packages.config b/Test/packages.config
index cab5134c1..5d12edde5 100644
--- a/Test/packages.config
+++ b/Test/packages.config
@@ -3,4 +3,5 @@
   <package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
   <package id="NUnit" version="3.6.1" targetFramework="net451" />
   <package id="NUnit3TestAdapter" version="3.7.0" targetFramework="net451" />
+  <package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
 </packages>
\ No newline at end of file
diff --git a/TestThermo/TestThermo.csproj b/TestThermo/TestThermo.csproj
index 8ee749719..a89e15bdd 100644
--- a/TestThermo/TestThermo.csproj
+++ b/TestThermo/TestThermo.csproj
@@ -33,6 +33,9 @@
     <CodeAnalysisRuleSet>MinimumRecommendedRules.ruleset</CodeAnalysisRuleSet>
   </PropertyGroup>
   <ItemGroup>
+    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
+    </Reference>
     <Reference Include="nunit.framework, Version=3.6.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
       <HintPath>..\packages\NUnit.3.6.1\lib\net45\nunit.framework.dll</HintPath>
     </Reference>
@@ -44,6 +47,9 @@
     <Reference Include="System.Data" />
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
+    <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
+    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="TestThermo.cs" />
@@ -56,26 +62,26 @@
     </None>
   </ItemGroup>
   <ItemGroup>
+    <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj">
+      <Project>{6febb7ed-0be6-4493-817e-cefd4cbe61dd}</Project>
+      <Name>MassSpectrometry</Name>
+    </ProjectReference>
     <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}</Project>
       <Name>MzLibUtil</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpecFiles\MzML\MzML.csproj">
-      <Project>{012434FB-88A9-4DEC-B887-5F64C0B481D4}</Project>
+    <ProjectReference Include="..\MzML\MzML.csproj">
+      <Project>{012434fb-88a9-4dec-b887-5f64c0b481d4}</Project>
       <Name>MzML</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpecFiles\Thermo\Thermo.csproj">
-      <Project>{24DC85FF-E97B-4140-9614-77DD8FDDD32F}</Project>
-      <Name>Thermo</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpectrometry\MassSpectrometry.csproj">
-      <Project>{6febb7ed-0be6-4493-817e-cefd4cbe61dd}</Project>
-      <Name>MassSpectrometry</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\Spectra\Spectra.csproj">
-      <Project>{088e4fcb-d580-4bad-a811-a1796a7666d2}</Project>
+    <ProjectReference Include="..\Spectra\Spectra.csproj">
+      <Project>{088E4FCB-D580-4BAD-A811-A1796A7666D2}</Project>
       <Name>Spectra</Name>
     </ProjectReference>
+    <ProjectReference Include="..\Thermo\Thermo.csproj">
+      <Project>{24dc85ff-e97b-4140-9614-77dd8fddd32f}</Project>
+      <Name>Thermo</Name>
+    </ProjectReference>
   </ItemGroup>
   <ItemGroup>
     <Service Include="{82A7F48D-3B50-4B1E-B82E-3ADA8210C358}" />
diff --git a/TestThermo/packages.config b/TestThermo/packages.config
index 52968fd2f..5d12edde5 100644
--- a/TestThermo/packages.config
+++ b/TestThermo/packages.config
@@ -1,5 +1,7 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
+  <package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
   <package id="NUnit" version="3.6.1" targetFramework="net451" />
   <package id="NUnit3TestAdapter" version="3.7.0" targetFramework="net451" />
+  <package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
 </packages>
\ No newline at end of file
diff --git a/mzLib/MassSpecFiles/Thermo/IThermoScan.cs b/Thermo/IThermoScan.cs
similarity index 100%
rename from mzLib/MassSpecFiles/Thermo/IThermoScan.cs
rename to Thermo/IThermoScan.cs
diff --git a/mzLib/MassSpecFiles/Thermo/Properties/AssemblyInfo.cs b/Thermo/Properties/AssemblyInfo.cs
similarity index 100%
rename from mzLib/MassSpecFiles/Thermo/Properties/AssemblyInfo.cs
rename to Thermo/Properties/AssemblyInfo.cs
diff --git a/mzLib/MassSpecFiles/Thermo/Thermo.csproj b/Thermo/Thermo.csproj
similarity index 88%
rename from mzLib/MassSpecFiles/Thermo/Thermo.csproj
rename to Thermo/Thermo.csproj
index 8a98728f9..e77064473 100644
--- a/mzLib/MassSpecFiles/Thermo/Thermo.csproj
+++ b/Thermo/Thermo.csproj
@@ -29,9 +29,8 @@
     <OutputPath>bin\x64\Debug\</OutputPath>
   </PropertyGroup>
   <ItemGroup>
-    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\..\..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
-      <Private>True</Private>
+    <Reference Include="nunit.framework, Version=3.6.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
+      <HintPath>..\packages\NUnit.3.6.1\lib\net45\nunit.framework.dll</HintPath>
     </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
@@ -53,19 +52,19 @@
     <Compile Include="ThermoSpectrum.cs" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\..\..\ClassLibrary1\ClassLibrary1.vcxproj">
+    <ProjectReference Include="..\ManagedThermoHelperLayer\ClassLibrary1.vcxproj">
       <Project>{cdd56f70-d42f-4e86-a232-65f955cef6ec}</Project>
       <Name>ManagedThermoHelperLayer</Name>
     </ProjectReference>
-    <ProjectReference Include="..\..\..\MzLibUtil\MzLibUtil.csproj">
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}</Project>
       <Name>MzLibUtil</Name>
     </ProjectReference>
-    <ProjectReference Include="..\..\MassSpectrometry\MassSpectrometry.csproj">
+    <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj">
       <Project>{6febb7ed-0be6-4493-817e-cefd4cbe61dd}</Project>
       <Name>MassSpectrometry</Name>
     </ProjectReference>
-    <ProjectReference Include="..\..\Spectra\Spectra.csproj">
+    <ProjectReference Include="..\Spectra\Spectra.csproj">
       <Project>{088e4fcb-d580-4bad-a811-a1796a7666d2}</Project>
       <Name>Spectra</Name>
     </ProjectReference>
@@ -74,9 +73,6 @@
       <Name>MzML</Name>
     </ProjectReference>
   </ItemGroup>
-  <ItemGroup>
-    <None Include="packages.config" />
-  </ItemGroup>
   <ItemGroup>
     <COMReference Include="MSFileReaderLib">
       <Guid>{F0C5F3E3-4F2A-443E-A74D-0AABE3237494}</Guid>
@@ -88,6 +84,9 @@
       <EmbedInteropTypes>True</EmbedInteropTypes>
     </COMReference>
   </ItemGroup>
+  <ItemGroup>
+    <None Include="packages.config" />
+  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <PropertyGroup>
     <PreBuildEvent>xcopy /y /d  "$(SolutionDir)x64\$(Configuration)\*.dll" "$(ProjectDir)$(OutDir)"</PreBuildEvent>
diff --git a/mzLib/MassSpecFiles/Thermo/ThermoDynamicData.cs b/Thermo/ThermoDynamicData.cs
similarity index 100%
rename from mzLib/MassSpecFiles/Thermo/ThermoDynamicData.cs
rename to Thermo/ThermoDynamicData.cs
diff --git a/mzLib/MassSpecFiles/Thermo/ThermoFile.cs b/Thermo/ThermoFile.cs
similarity index 100%
rename from mzLib/MassSpecFiles/Thermo/ThermoFile.cs
rename to Thermo/ThermoFile.cs
diff --git a/mzLib/MassSpecFiles/Thermo/ThermoGlobalParams.cs b/Thermo/ThermoGlobalParams.cs
similarity index 100%
rename from mzLib/MassSpecFiles/Thermo/ThermoGlobalParams.cs
rename to Thermo/ThermoGlobalParams.cs
diff --git a/mzLib/MassSpecFiles/Thermo/ThermoMzPeak.cs b/Thermo/ThermoMzPeak.cs
similarity index 100%
rename from mzLib/MassSpecFiles/Thermo/ThermoMzPeak.cs
rename to Thermo/ThermoMzPeak.cs
diff --git a/mzLib/MassSpecFiles/Thermo/ThermoReadException.cs b/Thermo/ThermoReadException.cs
similarity index 100%
rename from mzLib/MassSpecFiles/Thermo/ThermoReadException.cs
rename to Thermo/ThermoReadException.cs
diff --git a/mzLib/MassSpecFiles/Thermo/ThermoScan.cs b/Thermo/ThermoScan.cs
similarity index 100%
rename from mzLib/MassSpecFiles/Thermo/ThermoScan.cs
rename to Thermo/ThermoScan.cs
diff --git a/mzLib/MassSpecFiles/Thermo/ThermoScanWithPrecursor.cs b/Thermo/ThermoScanWithPrecursor.cs
similarity index 100%
rename from mzLib/MassSpecFiles/Thermo/ThermoScanWithPrecursor.cs
rename to Thermo/ThermoScanWithPrecursor.cs
diff --git a/mzLib/MassSpecFiles/Thermo/ThermoSpectrum.cs b/Thermo/ThermoSpectrum.cs
similarity index 100%
rename from mzLib/MassSpecFiles/Thermo/ThermoSpectrum.cs
rename to Thermo/ThermoSpectrum.cs
diff --git a/mzLib/MassSpecFiles/Thermo/ThermoStaticData.cs b/Thermo/ThermoStaticData.cs
similarity index 100%
rename from mzLib/MassSpecFiles/Thermo/ThermoStaticData.cs
rename to Thermo/ThermoStaticData.cs
diff --git a/Thermo/packages.config b/Thermo/packages.config
new file mode 100644
index 000000000..17c46bab0
--- /dev/null
+++ b/Thermo/packages.config
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="utf-8"?>
+<packages>
+  <package id="NUnit" version="3.6.1" targetFramework="net451" />
+</packages>
\ No newline at end of file
diff --git a/Win32Project8/ReadMe.txt b/UnmanagedThermoHelperLayer/ReadMe.txt
similarity index 100%
rename from Win32Project8/ReadMe.txt
rename to UnmanagedThermoHelperLayer/ReadMe.txt
diff --git a/Win32Project8/Win32Project8.cpp b/UnmanagedThermoHelperLayer/Win32Project8.cpp
similarity index 100%
rename from Win32Project8/Win32Project8.cpp
rename to UnmanagedThermoHelperLayer/Win32Project8.cpp
diff --git a/Win32Project8/Win32Project8.h b/UnmanagedThermoHelperLayer/Win32Project8.h
similarity index 100%
rename from Win32Project8/Win32Project8.h
rename to UnmanagedThermoHelperLayer/Win32Project8.h
diff --git a/Win32Project8/Win32Project8.vcxproj b/UnmanagedThermoHelperLayer/Win32Project8.vcxproj
similarity index 100%
rename from Win32Project8/Win32Project8.vcxproj
rename to UnmanagedThermoHelperLayer/Win32Project8.vcxproj
diff --git a/Win32Project8/Win32Project8.vcxproj.filters b/UnmanagedThermoHelperLayer/Win32Project8.vcxproj.filters
similarity index 100%
rename from Win32Project8/Win32Project8.vcxproj.filters
rename to UnmanagedThermoHelperLayer/Win32Project8.vcxproj.filters
diff --git a/Win32Project8/dllmain.cpp b/UnmanagedThermoHelperLayer/dllmain.cpp
similarity index 100%
rename from Win32Project8/dllmain.cpp
rename to UnmanagedThermoHelperLayer/dllmain.cpp
diff --git a/Win32Project8/stdafx.cpp b/UnmanagedThermoHelperLayer/stdafx.cpp
similarity index 100%
rename from Win32Project8/stdafx.cpp
rename to UnmanagedThermoHelperLayer/stdafx.cpp
diff --git a/Win32Project8/stdafx.h b/UnmanagedThermoHelperLayer/stdafx.h
similarity index 100%
rename from Win32Project8/stdafx.h
rename to UnmanagedThermoHelperLayer/stdafx.h
diff --git a/Win32Project8/targetver.h b/UnmanagedThermoHelperLayer/targetver.h
similarity index 100%
rename from Win32Project8/targetver.h
rename to UnmanagedThermoHelperLayer/targetver.h
diff --git a/mzLib/UsefulProteomicsDatabases/Generated/PsiModGenerated.cs b/UsefulProteomicsDatabases/Generated/PsiModGenerated.cs
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/Generated/PsiModGenerated.cs
rename to UsefulProteomicsDatabases/Generated/PsiModGenerated.cs
diff --git a/mzLib/UsefulProteomicsDatabases/Generated/unimod_2.cs b/UsefulProteomicsDatabases/Generated/unimod_2.cs
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/Generated/unimod_2.cs
rename to UsefulProteomicsDatabases/Generated/unimod_2.cs
diff --git a/mzLib/UsefulProteomicsDatabases/Loaders.cs b/UsefulProteomicsDatabases/Loaders.cs
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/Loaders.cs
rename to UsefulProteomicsDatabases/Loaders.cs
diff --git a/mzLib/UsefulProteomicsDatabases/PeriodicTableLoader.cs b/UsefulProteomicsDatabases/PeriodicTableLoader.cs
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/PeriodicTableLoader.cs
rename to UsefulProteomicsDatabases/PeriodicTableLoader.cs
diff --git a/mzLib/UsefulProteomicsDatabases/Properties/AssemblyInfo.cs b/UsefulProteomicsDatabases/Properties/AssemblyInfo.cs
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/Properties/AssemblyInfo.cs
rename to UsefulProteomicsDatabases/Properties/AssemblyInfo.cs
diff --git a/mzLib/UsefulProteomicsDatabases/ProteinDbLoader.cs b/UsefulProteomicsDatabases/ProteinDbLoader.cs
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/ProteinDbLoader.cs
rename to UsefulProteomicsDatabases/ProteinDbLoader.cs
diff --git a/mzLib/UsefulProteomicsDatabases/ProteinDbWriter.cs b/UsefulProteomicsDatabases/ProteinDbWriter.cs
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/ProteinDbWriter.cs
rename to UsefulProteomicsDatabases/ProteinDbWriter.cs
diff --git a/mzLib/UsefulProteomicsDatabases/PtmListLoader.cs b/UsefulProteomicsDatabases/PtmListLoader.cs
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/PtmListLoader.cs
rename to UsefulProteomicsDatabases/PtmListLoader.cs
diff --git a/mzLib/UsefulProteomicsDatabases/PtmListLoaderException.cs b/UsefulProteomicsDatabases/PtmListLoaderException.cs
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/PtmListLoaderException.cs
rename to UsefulProteomicsDatabases/PtmListLoaderException.cs
diff --git a/mzLib/UsefulProteomicsDatabases/UnimodLoader.cs b/UsefulProteomicsDatabases/UnimodLoader.cs
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/UnimodLoader.cs
rename to UsefulProteomicsDatabases/UnimodLoader.cs
diff --git a/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj b/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj
similarity index 90%
rename from mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj
rename to UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj
index 0fd39b39f..cb40a0833 100644
--- a/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj
+++ b/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj
@@ -33,9 +33,8 @@
     <CodeAnalysisRuleSet>MinimumRecommendedRules.ruleset</CodeAnalysisRuleSet>
   </PropertyGroup>
   <ItemGroup>
-    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
-      <Private>True</Private>
+    <Reference Include="nunit.framework, Version=3.6.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
+      <HintPath>..\packages\NUnit.3.6.1\lib\net45\nunit.framework.dll</HintPath>
     </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
@@ -49,8 +48,7 @@
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
     <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
-      <Private>True</Private>
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
     </Reference>
   </ItemGroup>
   <ItemGroup>
diff --git a/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.nuspec b/UsefulProteomicsDatabases/UsefulProteomicsDatabases.nuspec
similarity index 100%
rename from mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.nuspec
rename to UsefulProteomicsDatabases/UsefulProteomicsDatabases.nuspec
diff --git a/UsefulProteomicsDatabases/packages.config b/UsefulProteomicsDatabases/packages.config
new file mode 100644
index 000000000..cafbdeab9
--- /dev/null
+++ b/UsefulProteomicsDatabases/packages.config
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="utf-8"?>
+<packages>
+  <package id="NUnit" version="3.6.1" targetFramework="net451" />
+  <package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
+</packages>
\ No newline at end of file
diff --git a/mzLib/MassSpecFiles/mzIdentML/MzidIdentifications.cs b/mzIdentML/MzidIdentifications.cs
similarity index 100%
rename from mzLib/MassSpecFiles/mzIdentML/MzidIdentifications.cs
rename to mzIdentML/MzidIdentifications.cs
diff --git a/mzLib/MassSpecFiles/mzIdentML/Properties/AssemblyInfo.cs b/mzIdentML/Properties/AssemblyInfo.cs
similarity index 100%
rename from mzLib/MassSpecFiles/mzIdentML/Properties/AssemblyInfo.cs
rename to mzIdentML/Properties/AssemblyInfo.cs
diff --git a/mzLib/MassSpecFiles/mzIdentML/mzIdentML.csproj b/mzIdentML/mzIdentML.csproj
similarity index 93%
rename from mzLib/MassSpecFiles/mzIdentML/mzIdentML.csproj
rename to mzIdentML/mzIdentML.csproj
index 681479ce0..ebc64c470 100644
--- a/mzLib/MassSpecFiles/mzIdentML/mzIdentML.csproj
+++ b/mzIdentML/mzIdentML.csproj
@@ -50,15 +50,15 @@
     </Compile>
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\..\..\MzLibUtil\MzLibUtil.csproj">
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{b208ff5f-5a33-490d-9ddb-7c76f5600fc4}</Project>
       <Name>MzLibUtil</Name>
     </ProjectReference>
-    <ProjectReference Include="..\..\MassSpectrometry\MassSpectrometry.csproj">
+    <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj">
       <Project>{6febb7ed-0be6-4493-817e-cefd4cbe61dd}</Project>
       <Name>MassSpectrometry</Name>
     </ProjectReference>
-    <ProjectReference Include="..\..\Spectra\Spectra.csproj">
+    <ProjectReference Include="..\Spectra\Spectra.csproj">
       <Project>{088e4fcb-d580-4bad-a811-a1796a7666d2}</Project>
       <Name>Spectra</Name>
     </ProjectReference>
diff --git a/mzLib/MassSpecFiles/mzIdentML/mzIdentML1_1_0.cs b/mzIdentML/mzIdentML1_1_0.cs
similarity index 100%
rename from mzLib/MassSpecFiles/mzIdentML/mzIdentML1_1_0.cs
rename to mzIdentML/mzIdentML1_1_0.cs
diff --git a/mzLib/MassSpecFiles/mzIdentML/mzIdentML1_1_1.cs b/mzIdentML/mzIdentML1_1_1.cs
similarity index 100%
rename from mzLib/MassSpecFiles/mzIdentML/mzIdentML1_1_1.cs
rename to mzIdentML/mzIdentML1_1_1.cs
diff --git a/mzLib.nuspec b/mzLib.nuspec
index d3363fece..4bab285b8 100644
--- a/mzLib.nuspec
+++ b/mzLib.nuspec
@@ -28,8 +28,8 @@
     <file src="mzLib\Spectra\bin\x64\Release\Spectra.dll" target="lib" /> 
     <file src="mzLib\UsefulProteomicsDatabases\bin\x64\Release\UsefulProteomicsDatabases.dll" target="lib" /> 
     <file src="MzLibUtil\bin\x64\Release\MzLibUtil.dll" target="lib" /> 
-    <file src="x64\Release\ClassLibrary1.dll" target="lib" /> 
-    <file src="x64\Release\Win32Project8.dll" target="build" /> 
+    <file src="x64\Release\ManagedThermoHelperLayer.dll" target="lib" /> 
+    <file src="x64\Release\UnmanagedThermoHelperLayer.dll" target="build" /> 
     <file src="mzLib.targets" target="build" />
   </files>
 </package>
diff --git a/mzLib.sln b/mzLib.sln
index 7e4a56e1f..f8c6ea524 100644
--- a/mzLib.sln
+++ b/mzLib.sln
@@ -9,25 +9,12 @@ Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Benchmark", "Benchmark\Benc
 		{CDD56F70-D42F-4E86-A232-65F955CEF6EC} = {CDD56F70-D42F-4E86-A232-65F955CEF6EC}
 	EndProjectSection
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Chemistry", "mzLib\Chemistry\Chemistry.csproj", "{CBE368BB-FC84-458D-8099-87A63D17AA3B}"
-EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "mzIdentML", "mzLib\MassSpecFiles\mzIdentML\mzIdentML.csproj", "{63D869DF-55D8-4043-AD89-F90462403EBB}"
-EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "MzML", "mzLib\MassSpecFiles\MzML\MzML.csproj", "{012434FB-88A9-4DEC-B887-5F64C0B481D4}"
-EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Thermo", "mzLib\MassSpecFiles\Thermo\Thermo.csproj", "{24DC85FF-E97B-4140-9614-77DD8FDDD32F}"
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Test", "Test\Test.csproj", "{D7C69058-1FE4-49BD-B994-B08C1DFB21A4}"
 	ProjectSection(ProjectDependencies) = postProject
-		{8913A108-5D93-4AF7-B273-89A06E817611} = {8913A108-5D93-4AF7-B273-89A06E817611}
+		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD} = {6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}
+		{012434FB-88A9-4DEC-B887-5F64C0B481D4} = {012434FB-88A9-4DEC-B887-5F64C0B481D4}
 	EndProjectSection
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "MassSpectrometry", "mzLib\MassSpectrometry\MassSpectrometry.csproj", "{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}"
-EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Proteomics", "mzLib\Proteomics\Proteomics.csproj", "{4AB6BA94-B70C-4570-9EA6-165746D5B8E8}"
-EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Spectra", "mzLib\Spectra\Spectra.csproj", "{088E4FCB-D580-4BAD-A811-A1796A7666D2}"
-EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Test", "Test\Test.csproj", "{D7C69058-1FE4-49BD-B994-B08C1DFB21A4}"
-EndProject
 Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "TestThermo", "TestThermo\TestThermo.csproj", "{0FA1E770-6D5E-421B-802C-FDCA44791EAA}"
 	ProjectSection(ProjectDependencies) = postProject
 		{8913A108-5D93-4AF7-B273-89A06E817611} = {8913A108-5D93-4AF7-B273-89A06E817611}
@@ -36,99 +23,145 @@ Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "TestThermo", "TestThermo\Te
 EndProject
 Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "MzLibUtil", "MzLibUtil\MzLibUtil.csproj", "{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "UsefulProteomicsDatabases", "mzLib\UsefulProteomicsDatabases\UsefulProteomicsDatabases.csproj", "{16F857B5-4942-4FA2-B198-BD4D14C1B2E4}"
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Chemistry", "Chemistry\Chemistry.csproj", "{CBE368BB-FC84-458D-8099-87A63D17AA3B}"
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ManagedThermoHelperLayer", "ManagedThermoHelperLayer\ClassLibrary1.vcxproj", "{CDD56F70-D42F-4E86-A232-65F955CEF6EC}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "MassSpectrometry", "MassSpectrometry\MassSpectrometry.csproj", "{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}"
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "Win32Project8", "Win32Project8\Win32Project8.vcxproj", "{8913A108-5D93-4AF7-B273-89A06E817611}"
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "mzIdentML", "mzIdentML\mzIdentML.csproj", "{63D869DF-55D8-4043-AD89-F90462403EBB}"
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ClassLibrary1", "ClassLibrary1\ClassLibrary1.vcxproj", "{CDD56F70-D42F-4E86-A232-65F955CEF6EC}"
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "MzML", "MzML\MzML.csproj", "{012434FB-88A9-4DEC-B887-5F64C0B481D4}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Proteomics", "Proteomics\Proteomics.csproj", "{4AB6BA94-B70C-4570-9EA6-165746D5B8E8}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Spectra", "Spectra\Spectra.csproj", "{088E4FCB-D580-4BAD-A811-A1796A7666D2}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Thermo", "Thermo\Thermo.csproj", "{24DC85FF-E97B-4140-9614-77DD8FDDD32F}"
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "UnmanagedThermoHelperLayer", "UnmanagedThermoHelperLayer\Win32Project8.vcxproj", "{8913A108-5D93-4AF7-B273-89A06E817611}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "UsefulProteomicsDatabases", "UsefulProteomicsDatabases\UsefulProteomicsDatabases.csproj", "{16F857B5-4942-4FA2-B198-BD4D14C1B2E4}"
 EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|x64 = Debug|x64
+		Release|x64 = Release|x64
 		TestAndRelease|x64 = TestAndRelease|x64
 		TestAndReleaseNoThermo|x64 = TestAndReleaseNoThermo|x64
 	EndGlobalSection
 	GlobalSection(ProjectConfigurationPlatforms) = postSolution
 		{1B73064F-F8F8-44BE-9BDA-986A543DD72A}.Debug|x64.ActiveCfg = Debug|x64
 		{1B73064F-F8F8-44BE-9BDA-986A543DD72A}.Debug|x64.Build.0 = Debug|x64
+		{1B73064F-F8F8-44BE-9BDA-986A543DD72A}.Release|x64.ActiveCfg = Release|x64
+		{1B73064F-F8F8-44BE-9BDA-986A543DD72A}.Release|x64.Build.0 = Release|x64
 		{1B73064F-F8F8-44BE-9BDA-986A543DD72A}.TestAndRelease|x64.ActiveCfg = Release|x64
 		{1B73064F-F8F8-44BE-9BDA-986A543DD72A}.TestAndRelease|x64.Build.0 = Release|x64
 		{1B73064F-F8F8-44BE-9BDA-986A543DD72A}.TestAndReleaseNoThermo|x64.ActiveCfg = Release|x64
 		{1B73064F-F8F8-44BE-9BDA-986A543DD72A}.TestAndReleaseNoThermo|x64.Build.0 = Release|x64
+		{D7C69058-1FE4-49BD-B994-B08C1DFB21A4}.Debug|x64.ActiveCfg = Debug|x64
+		{D7C69058-1FE4-49BD-B994-B08C1DFB21A4}.Debug|x64.Build.0 = Debug|x64
+		{D7C69058-1FE4-49BD-B994-B08C1DFB21A4}.Release|x64.ActiveCfg = Release|x64
+		{D7C69058-1FE4-49BD-B994-B08C1DFB21A4}.Release|x64.Build.0 = Release|x64
+		{D7C69058-1FE4-49BD-B994-B08C1DFB21A4}.TestAndRelease|x64.ActiveCfg = Release|x64
+		{D7C69058-1FE4-49BD-B994-B08C1DFB21A4}.TestAndRelease|x64.Build.0 = Release|x64
+		{D7C69058-1FE4-49BD-B994-B08C1DFB21A4}.TestAndReleaseNoThermo|x64.ActiveCfg = Release|x64
+		{D7C69058-1FE4-49BD-B994-B08C1DFB21A4}.TestAndReleaseNoThermo|x64.Build.0 = Release|x64
+		{0FA1E770-6D5E-421B-802C-FDCA44791EAA}.Debug|x64.ActiveCfg = Debug|x64
+		{0FA1E770-6D5E-421B-802C-FDCA44791EAA}.Debug|x64.Build.0 = Debug|x64
+		{0FA1E770-6D5E-421B-802C-FDCA44791EAA}.Release|x64.ActiveCfg = Release|x64
+		{0FA1E770-6D5E-421B-802C-FDCA44791EAA}.Release|x64.Build.0 = Release|x64
+		{0FA1E770-6D5E-421B-802C-FDCA44791EAA}.TestAndRelease|x64.ActiveCfg = Release|x64
+		{0FA1E770-6D5E-421B-802C-FDCA44791EAA}.TestAndRelease|x64.Build.0 = Release|x64
+		{0FA1E770-6D5E-421B-802C-FDCA44791EAA}.TestAndReleaseNoThermo|x64.ActiveCfg = Release|x64
+		{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}.Debug|x64.ActiveCfg = Debug|x64
+		{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}.Debug|x64.Build.0 = Debug|x64
+		{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}.Release|x64.ActiveCfg = Release|x64
+		{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}.Release|x64.Build.0 = Release|x64
+		{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}.TestAndRelease|x64.ActiveCfg = Release|x64
+		{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}.TestAndRelease|x64.Build.0 = Release|x64
+		{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}.TestAndReleaseNoThermo|x64.ActiveCfg = Release|x64
+		{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}.TestAndReleaseNoThermo|x64.Build.0 = Release|x64
 		{CBE368BB-FC84-458D-8099-87A63D17AA3B}.Debug|x64.ActiveCfg = Debug|x64
 		{CBE368BB-FC84-458D-8099-87A63D17AA3B}.Debug|x64.Build.0 = Debug|x64
+		{CBE368BB-FC84-458D-8099-87A63D17AA3B}.Release|x64.ActiveCfg = Release|x64
+		{CBE368BB-FC84-458D-8099-87A63D17AA3B}.Release|x64.Build.0 = Release|x64
 		{CBE368BB-FC84-458D-8099-87A63D17AA3B}.TestAndRelease|x64.ActiveCfg = Release|x64
 		{CBE368BB-FC84-458D-8099-87A63D17AA3B}.TestAndRelease|x64.Build.0 = Release|x64
 		{CBE368BB-FC84-458D-8099-87A63D17AA3B}.TestAndReleaseNoThermo|x64.ActiveCfg = Release|x64
 		{CBE368BB-FC84-458D-8099-87A63D17AA3B}.TestAndReleaseNoThermo|x64.Build.0 = Release|x64
+		{CDD56F70-D42F-4E86-A232-65F955CEF6EC}.Debug|x64.ActiveCfg = Debug|x64
+		{CDD56F70-D42F-4E86-A232-65F955CEF6EC}.Debug|x64.Build.0 = Debug|x64
+		{CDD56F70-D42F-4E86-A232-65F955CEF6EC}.Release|x64.ActiveCfg = Release|x64
+		{CDD56F70-D42F-4E86-A232-65F955CEF6EC}.Release|x64.Build.0 = Release|x64
+		{CDD56F70-D42F-4E86-A232-65F955CEF6EC}.TestAndRelease|x64.ActiveCfg = Release|x64
+		{CDD56F70-D42F-4E86-A232-65F955CEF6EC}.TestAndRelease|x64.Build.0 = Release|x64
+		{CDD56F70-D42F-4E86-A232-65F955CEF6EC}.TestAndReleaseNoThermo|x64.ActiveCfg = Release|x64
+		{CDD56F70-D42F-4E86-A232-65F955CEF6EC}.TestAndReleaseNoThermo|x64.Build.0 = Release|x64
+		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}.Debug|x64.ActiveCfg = Debug|x64
+		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}.Debug|x64.Build.0 = Debug|x64
+		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}.Release|x64.ActiveCfg = Release|x64
+		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}.Release|x64.Build.0 = Release|x64
+		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}.TestAndRelease|x64.ActiveCfg = Release|x64
+		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}.TestAndRelease|x64.Build.0 = Release|x64
+		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}.TestAndReleaseNoThermo|x64.ActiveCfg = Release|x64
+		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}.TestAndReleaseNoThermo|x64.Build.0 = Release|x64
 		{63D869DF-55D8-4043-AD89-F90462403EBB}.Debug|x64.ActiveCfg = Debug|x64
 		{63D869DF-55D8-4043-AD89-F90462403EBB}.Debug|x64.Build.0 = Debug|x64
+		{63D869DF-55D8-4043-AD89-F90462403EBB}.Release|x64.ActiveCfg = Release|x64
+		{63D869DF-55D8-4043-AD89-F90462403EBB}.Release|x64.Build.0 = Release|x64
 		{63D869DF-55D8-4043-AD89-F90462403EBB}.TestAndRelease|x64.ActiveCfg = Release|x64
 		{63D869DF-55D8-4043-AD89-F90462403EBB}.TestAndRelease|x64.Build.0 = Release|x64
 		{63D869DF-55D8-4043-AD89-F90462403EBB}.TestAndReleaseNoThermo|x64.ActiveCfg = Release|x64
 		{63D869DF-55D8-4043-AD89-F90462403EBB}.TestAndReleaseNoThermo|x64.Build.0 = Release|x64
 		{012434FB-88A9-4DEC-B887-5F64C0B481D4}.Debug|x64.ActiveCfg = Debug|x64
 		{012434FB-88A9-4DEC-B887-5F64C0B481D4}.Debug|x64.Build.0 = Debug|x64
+		{012434FB-88A9-4DEC-B887-5F64C0B481D4}.Release|x64.ActiveCfg = Release|x64
+		{012434FB-88A9-4DEC-B887-5F64C0B481D4}.Release|x64.Build.0 = Release|x64
 		{012434FB-88A9-4DEC-B887-5F64C0B481D4}.TestAndRelease|x64.ActiveCfg = Release|x64
 		{012434FB-88A9-4DEC-B887-5F64C0B481D4}.TestAndRelease|x64.Build.0 = Release|x64
 		{012434FB-88A9-4DEC-B887-5F64C0B481D4}.TestAndReleaseNoThermo|x64.ActiveCfg = Release|x64
 		{012434FB-88A9-4DEC-B887-5F64C0B481D4}.TestAndReleaseNoThermo|x64.Build.0 = Release|x64
-		{24DC85FF-E97B-4140-9614-77DD8FDDD32F}.Debug|x64.ActiveCfg = Debug|x64
-		{24DC85FF-E97B-4140-9614-77DD8FDDD32F}.Debug|x64.Build.0 = Debug|x64
-		{24DC85FF-E97B-4140-9614-77DD8FDDD32F}.TestAndRelease|x64.ActiveCfg = Release|x64
-		{24DC85FF-E97B-4140-9614-77DD8FDDD32F}.TestAndRelease|x64.Build.0 = Release|x64
-		{24DC85FF-E97B-4140-9614-77DD8FDDD32F}.TestAndReleaseNoThermo|x64.ActiveCfg = Release|x64
-		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}.Debug|x64.ActiveCfg = Debug|x64
-		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}.Debug|x64.Build.0 = Debug|x64
-		{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}.TestAndRelease|x64.ActiveCfg = Release|x64
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 		{4AB6BA94-B70C-4570-9EA6-165746D5B8E8}.Debug|x64.Build.0 = Debug|x64
+		{4AB6BA94-B70C-4570-9EA6-165746D5B8E8}.Release|x64.ActiveCfg = Release|x64
+		{4AB6BA94-B70C-4570-9EA6-165746D5B8E8}.Release|x64.Build.0 = Release|x64
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 		{088E4FCB-D580-4BAD-A811-A1796A7666D2}.Debug|x64.Build.0 = Debug|x64
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-		{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}.TestAndReleaseNoThermo|x64.Build.0 = Release|x64
+		{24DC85FF-E97B-4140-9614-77DD8FDDD32F}.Debug|x64.ActiveCfg = Debug|x64
+		{24DC85FF-E97B-4140-9614-77DD8FDDD32F}.Debug|x64.Build.0 = Debug|x64
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-		{CDD56F70-D42F-4E86-A232-65F955CEF6EC}.Debug|x64.Build.0 = Debug|x64
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-		{CDD56F70-D42F-4E86-A232-65F955CEF6EC}.TestAndRelease|x64.Build.0 = Release|x64
-		{CDD56F70-D42F-4E86-A232-65F955CEF6EC}.TestAndReleaseNoThermo|x64.ActiveCfg = Release|x64
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
diff --git a/mzLib.targets b/mzLib.targets
index 90e8b6f5f..5749677e7 100644
--- a/mzLib.targets
+++ b/mzLib.targets
@@ -2,7 +2,7 @@
 <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003"> 
   <Target Name="AfterBuild"> 
     <ItemGroup> 
-      <MyPackageFiles Include="$(MSBuildProjectDirectory)\..\Packages\**\build\Win32Project8.dll"/> 
+      <MyPackageFiles Include="$(MSBuildProjectDirectory)\..\Packages\**\build\UnmanagedThermoHelperLayer.dll"/> 
     </ItemGroup> 
     <Copy SourceFiles="@(MyPackageFiles)" DestinationFolder="$(OutputPath)" > 
     </Copy> 

From 949fa54b6d25c3c43ac4d2a275bcbfa5847cd99f Mon Sep 17 00:00:00 2001
From: stepa <stepa@ARES>
Date: Wed, 15 Mar 2017 17:37:24 -0500
Subject: [PATCH 2/3] hmh

---
 mzLib.nuspec | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/mzLib.nuspec b/mzLib.nuspec
index 4bab285b8..1cdde20fb 100644
--- a/mzLib.nuspec
+++ b/mzLib.nuspec
@@ -19,14 +19,14 @@
     </dependencies>
   </metadata>
   <files>
-    <file src="mzLib\Chemistry\bin\x64\Release\Chemistry.dll" target="lib" /> 
-    <file src="mzLib\MassSpecFiles\mzIdentML\bin\x64\Release\mzIdentML.dll" target="lib" /> 
-    <file src="mzLib\MassSpecFiles\MzML\bin\x64\Release\MzML.dll" target="lib" /> 
-    <file src="mzLib\MassSpecFiles\Thermo\bin\x64\Release\Thermo.dll" target="lib" /> 
-    <file src="mzLib\MassSpectrometry\bin\x64\Release\MassSpectrometry.dll" target="lib" /> 
-    <file src="mzLib\Proteomics\bin\x64\Release\Proteomics.dll" target="lib" /> 
-    <file src="mzLib\Spectra\bin\x64\Release\Spectra.dll" target="lib" /> 
-    <file src="mzLib\UsefulProteomicsDatabases\bin\x64\Release\UsefulProteomicsDatabases.dll" target="lib" /> 
+    <file src="Chemistry\bin\x64\Release\Chemistry.dll" target="lib" /> 
+    <file src="mzIdentML\bin\x64\Release\mzIdentML.dll" target="lib" /> 
+    <file src="MzML\bin\x64\Release\MzML.dll" target="lib" /> 
+    <file src="Thermo\bin\x64\Release\Thermo.dll" target="lib" /> 
+    <file src="MassSpectrometry\bin\x64\Release\MassSpectrometry.dll" target="lib" /> 
+    <file src="Proteomics\bin\x64\Release\Proteomics.dll" target="lib" /> 
+    <file src="Spectra\bin\x64\Release\Spectra.dll" target="lib" /> 
+    <file src="UsefulProteomicsDatabases\bin\x64\Release\UsefulProteomicsDatabases.dll" target="lib" /> 
     <file src="MzLibUtil\bin\x64\Release\MzLibUtil.dll" target="lib" /> 
     <file src="x64\Release\ManagedThermoHelperLayer.dll" target="lib" /> 
     <file src="x64\Release\UnmanagedThermoHelperLayer.dll" target="build" /> 

From 4d0654b427b36153d73858992d4b2a8c93d37865 Mon Sep 17 00:00:00 2001
From: stepa <stepa@ARES>
Date: Wed, 15 Mar 2017 17:41:49 -0500
Subject: [PATCH 3/3] uhum

---
 mzLib.sln | 29 -----------------------------
 1 file changed, 29 deletions(-)

diff --git a/mzLib.sln b/mzLib.sln
index f8c6ea524..97537c3b4 100644
--- a/mzLib.sln
+++ b/mzLib.sln
@@ -46,118 +46,89 @@ EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|x64 = Debug|x64
-		Release|x64 = Release|x64
 		TestAndRelease|x64 = TestAndRelease|x64
 		TestAndReleaseNoThermo|x64 = TestAndReleaseNoThermo|x64
 	EndGlobalSection
 	GlobalSection(ProjectConfigurationPlatforms) = postSolution
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